Binding Site Information of Target
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T46216 | Target Info | |||
| Target Name | Bromodomain-containing protein 9 (BRD9) | ||||
| Synonyms | Rhabdomyosarcoma antigen MU-RMS-40.8 | ||||
| Target Type | Literature-reported Target | ||||
| Gene Name | BRD9 | ||||
| Biochemical Class | Bromodomain | ||||
| UniProt ID | |||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| Ligand Name: Sunitinib | Ligand Info | |||||
| Structure Description | Crystal structure of the bromodomain of human BRD9 bound to sunitinib | PDB:6V0X | ||||
| Method | X-ray diffraction | Resolution | 1.50 Å | Mutation | No | [1] |
| PDB Sequence |
STPIQQLLEH
147 FLRQLQRKDP157 HGFFAFPVTD167 AIAPGYSMII177 KHPMDFGTMK187 DKIVANEYKS 197 VTEFKADFKL207 MCDNAMTYNR217 PDTVYYKLAK227 KILHAGFKM
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| Ligand Name: I-BRD9 | Ligand Info | |||||
| Structure Description | Crystal structure of the bromodomain of human BRD9 bound to I-BRD9 | PDB:6V1B | ||||
| Method | X-ray diffraction | Resolution | 1.35 Å | Mutation | No | [1] |
| PDB Sequence |
ESTPIQQLLE
146 HFLRQLQRKD156 PHGFFAFPVT166 DAIAPGYSMI176 IKHPMDFGTM186 KDKIVANEYK 196 SVTEFKADFK206 LMCDNAMTYN216 RPDTVYYKLA226 KKILHAGFKM236 MSKERLLALK 246 RSMS
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: BI 7273 | Ligand Info | |||||
| Structure Description | CRYSTAL STRUCTURE OF BRD9 IN COMPLEX WITH BI-7273 | PDB:5EU1 | ||||
| Method | X-ray diffraction | Resolution | 1.60 Å | Mutation | No | [2] |
| PDB Sequence |
STPIQQLLEH
31 FLRQLQRKDP41 HGFFAFPVTD51 AIAPGYSMII61 KHPMDFGTMK71 DKIVANEYKS 81 VTEFKADFKL91 MCDNAMTYNR101 PDTVYYKLAK111 KILHAGFKMM121 SKERLLALKR 131 SMS
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .5SW or .5SW2 or .5SW3 or :35SW;style chemicals stick;color identity;select .A:42 or .A:43 or .A:44 or .A:45 or .A:46 or .A:47 or .A:48 or .A:49 or .A:53 or .A:54 or .A:57 or .A:96 or .A:99 or .A:100 or .A:106; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: Bromosporine | Ligand Info | |||||
| Structure Description | Crystal structure of the bromodomain of human BRD9 in complex with bromosporine (BSP) | PDB:5IGM | ||||
| Method | X-ray diffraction | Resolution | 1.60 Å | Mutation | No | [3] |
| PDB Sequence |
STPIQQLLEH
147 FLRQLQRKDP157 HGFFAFPVTD167 AIAPGYSMII177 KHPMDFGTMK187 DKIVANEYKS 197 VTEFKADFKL207 MCDNAMTYNR217 PDTVYYKLAK227 KILHAGFKMM237 SKERLLALKR 247 SMS
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .BMF or .BMF2 or .BMF3 or :3BMF;style chemicals stick;color identity;select .A:159 or .A:160 or .A:161 or .A:162 or .A:163 or .A:164 or .A:165 or .A:169 or .A:170 or .A:171 or .A:173 or .A:212 or .A:215 or .A:216 or .A:222; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: LP99 | Ligand Info | |||||
| Structure Description | Crystal structure of human BRD9 bromodomain in complex with LP99 chemical probe | PDB:5IGN | ||||
| Method | X-ray diffraction | Resolution | 1.70 Å | Mutation | No | [4] |
| PDB Sequence |
STPIQQLLEH
31 FLRQLQRKDP41 HGFFAFPVTD51 AIAPGYSMII61 KHPMDFGTMK71 DKIVANEYKS 81 VTEFKADFKL91 MCDNAMTYNR101 PDTVYYKLAK111 KILHAGFKMM121 SKERLLALKR 131 SMS
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .6B2 or .6B22 or .6B23 or :36B2;style chemicals stick;color identity;select .A:42 or .A:43 or .A:44 or .A:45 or .A:46 or .A:47 or .A:48 or .A:49 or .A:50 or .A:53 or .A:54 or .A:57 or .A:96 or .A:99 or .A:100 or .A:106; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: PMID25703523C7d | Ligand Info | |||||
| Structure Description | Crystal Structure of the bromodomain of BRD9 in complex with a 2-amine-9H-purine ligand | PDB:4XY8 | ||||
| Method | X-ray diffraction | Resolution | 1.70 Å | Mutation | No | [5] |
| PDB Sequence |
STPIQQLLEH
31 FLRQLQRKDP41 HGFFAFPVTD51 AIAPGYSMII61 KHPMDFGTMK71 DKIVANEYKS 81 VTEFKADFKL91 MCDNAMTYNR101 PDTVYYKLAK111 KILHAGFKMM121 SKERLLALKR 131 SMS
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .43U or .43U2 or .43U3 or :343U;style chemicals stick;color identity;select .A:44 or .A:45 or .A:47 or .A:48 or .A:49 or .A:53 or .A:54 or .A:57 or .A:96 or .A:99 or .A:100 or .A:106; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: TG003 | Ligand Info | |||||
| Structure Description | Crystal structure of the bromodomain of human BRD9 bound to TG003 | PDB:6V0S | ||||
| Method | X-ray diffraction | Resolution | 2.40 Å | Mutation | No | [1] |
| PDB Sequence |
STPIQQLLEH
147 FLRQLQRKDP157 HGFFAFPVTD167 AIAPGYSMII177 KHPMDFGTMK187 DKIVANEYKS 197 VTEFKADFKL207 MCDNAMTYNR217 PDTVYYKLAK227 KILHAGFKMM237 SKERLLALKR 247 SMS
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .EAE or .EAE2 or .EAE3 or :3EAE;style chemicals stick;color identity;select .A:159 or .A:160 or .A:161 or .A:163 or .A:165 or .A:169 or .A:170 or .A:173 or .A:212 or .A:215 or .A:216 or .A:222; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 4-(1,5-Dimethyl-6-Oxidanylidene-Pyridin-3-Yl)benzamide | Ligand Info | |||||
| Structure Description | Crystal structure of the BRD9 bromodomain in complex with compound 4. | PDB:5F25 | ||||
| Method | X-ray diffraction | Resolution | 1.68 Å | Mutation | No | [2] |
| PDB Sequence |
STPIQQLLEH
31 FLRQLQRKDP41 HGFFAFPVTD51 AIAPGYSMII61 KHPMDFGTMK71 DKIVANEYKS 81 VTEFKADFKL91 MCDNAMTYNR101 PDTVYYKLAK111 KILHAGFKMM121 SKERLLALKR 131 SMS
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .5TU or .5TU2 or .5TU3 or :35TU;style chemicals stick;color identity;select .A:43 or .A:44 or .A:45 or .A:49 or .A:53 or .A:54 or .A:57 or .A:96 or .A:99 or .A:100 or .A:106; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 3-(6-Acetylpyrrolo[1,2-a]pyrimidin-8-yl)-N-cyclopropyl-4-methylbenzamide | Ligand Info | |||||
| Structure Description | Crystal structure of the bromodomain of human BRD9 bound to TP472 | PDB:6V14 | ||||
| Method | X-ray diffraction | Resolution | 1.70 Å | Mutation | No | [1] |
| PDB Sequence |
STPIQQLLEH
147 FLRQLQRKDP157 HGFFAFPVTD167 AIAPGYSMII177 KHPMDFGTMK187 DKIVANEYKS 197 VTEFKADFKL207 MCDNAMTYNR217 PDTVYYKLAK227 KILHAGFKMM237 SK |
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .QMG or .QMG2 or .QMG3 or :3QMG;style chemicals stick;color identity;select .A:159 or .A:160 or .A:161 or .A:163 or .A:165 or .A:169 or .A:170 or .A:173 or .A:212 or .A:215 or .A:216 or .A:222; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: 2-Chloro-N-[5-(3-Methyl[1,2,4]triazolo[3,4-A]phthalazin-6-Yl)-2-(Morpholin-4-Yl)phenyl]benzenesulfonamide | Ligand Info | |||||
| Structure Description | Crystal Structure of the bromodomain of human BRD9 in complex with a triazolo-phthalazine ligand | PDB:4NQN | ||||
| Method | X-ray diffraction | Resolution | 1.73 Å | Mutation | No | [6] |
| PDB Sequence |
ESTPIQQLLE
30 HFLRQLQRKD40 PHGFFAFPVT50 DAIAPGYSMI60 IKHPMDFGTM70 KDKIVANEYK 80 SVTEFKADFK90 LMCDNAMTYN100 RPDTVYYKLA110 KKILHAGFKM120 MSKERLLALK 130 RSM
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .Y1Z or .Y1Z2 or .Y1Z3 or :3Y1Z;style chemicals stick;color identity;select .A:42 or .A:43 or .A:44 or .A:45 or .A:49 or .A:53 or .A:54 or .A:57 or .A:96 or .A:99 or .A:100 or .A:106; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 1,4-Dimethyl-7-(2-Oxopiperidin-1-Yl)quinolin-2(1h)-One | Ligand Info | |||||
| Structure Description | Crystal structure of BRD9 bromodomain in complex with a valerolactam quinolone ligand | PDB:4Z6H | ||||
| Method | X-ray diffraction | Resolution | 1.80 Å | Mutation | No | [7] |
| PDB Sequence |
STPIQQLLEH
31 FLRQLQRKDP41 HGFFAFPVTD51 AIAPGYSMII61 KHPMDFGTMK71 DKIVANEYKS 81 VTEFKADFKL91 MCDNAMTYNR101 PDTVYYKLAK111 KILHAGFKMM121 SKERLLALKR 131 SMS
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .4L2 or .4L22 or .4L23 or :34L2;style chemicals stick;color identity;select .A:42 or .A:43 or .A:44 or .A:45 or .A:46 or .A:47 or .A:48 or .A:49 or .A:53 or .A:54 or .A:57 or .A:96 or .A:99 or .A:100 or .A:106; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 1-[1-(Imidazo[1,2-A]pyridin-5-Yl)-7-(Morpholin-4-Yl)indolizin-3-Yl]ethanone | Ligand Info | |||||
| Structure Description | Crystal structure of BRD9 bromodomain in complex with an indolizine ligand | PDB:5E9V | ||||
| Method | X-ray diffraction | Resolution | 1.80 Å | Mutation | No | [8] |
| PDB Sequence |
STPIQQLLEH
147 FLRQLQRKDP157 HGFFAFPVTD167 AIAPGYSMII177 KHPMDFGTMK187 DKIVANEYKS 197 VTEFKADFKL207 MCDNAMTYNR217 PDTVYYKLAK227 KILHAGFKMM237 SKERLLALKR 247 SMS
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .5L0 or .5L02 or .5L03 or :35L0;style chemicals stick;color identity;select .A:159 or .A:160 or .A:161 or .A:163 or .A:164 or .A:165 or .A:169 or .A:170 or .A:171 or .A:173 or .A:212 or .A:215 or .A:216 or .A:222; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 2-(Dimethylamino)-6-Methyl-Pyrido[4,3-D]pyrimidin-5-One | Ligand Info | |||||
| Structure Description | Crystal structure of the BRD9 bromodomain in complex with compound 3. | PDB:5F2P | ||||
| Method | X-ray diffraction | Resolution | 1.80 Å | Mutation | No | [2] |
| PDB Sequence |
STPIQQLLEH
31 FLRQLQRKDP41 HGFFAFPVTD51 AIAPGYSMII61 KHPMDFGTMK71 DKIVANEYKS 81 VTEFKADFKL91 MCDNAMTYNR101 PDTVYYKLAK111 KILHAGFKMM121 SKERLLALKR 131 SMS
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .5TY or .5TY2 or .5TY3 or :35TY;style chemicals stick;color identity;select .A:44 or .A:45 or .A:47 or .A:49 or .A:53 or .A:54 or .A:55 or .A:57 or .A:96 or .A:99 or .A:100 or .A:106; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 4-[4-[(Dimethylamino)methyl]-2,5-Dimethoxy-Phenyl]-2-Methyl-2,7-Naphthyridin-1-One | Ligand Info | |||||
| Structure Description | Crystal structure of the BRD9 bromodamian in complex with BI-9564. | PDB:5F1H | ||||
| Method | X-ray diffraction | Resolution | 1.82 Å | Mutation | No | [2] |
| PDB Sequence |
STPIQQLLEH
31 FLRQLQRKDP41 HGFFAFPVTD51 AIAPGYSMII61 KHPMDFGTMK71 DKIVANEYKS 81 VTEFKADFKL91 MCDNAMTYNR101 PDTVYYKLAK111 KILHAGFKMM121 SKERLLALKR 131 SMS
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .5U6 or .5U62 or .5U63 or :35U6;style chemicals stick;color identity;select .A:42 or .A:43 or .A:44 or .A:45 or .A:47 or .A:48 or .A:49 or .A:53 or .A:54 or .A:57 or .A:96 or .A:99 or .A:100 or .A:106; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: Tert-Butyl [(2r,3s)-1-(1,4-Dimethyl-2-Oxo-1,2-Dihydroquinolin-7-Yl)-6-Oxo-2-Phenylpiperidin-3-Yl]carbamate | Ligand Info | |||||
| Structure Description | Crystal structure of BRD9 bromodomain in complex with a substituted valerolactam quinolone ligand | PDB:4Z6I | ||||
| Method | X-ray diffraction | Resolution | 1.95 Å | Mutation | No | [7] |
| PDB Sequence |
STPIQQLLEH
31 FLRQLQRKDP41 HGFFAFPVTD51 AIAPGYSMII61 KHPMDFGTMK71 DKIVANEYKS 81 VTEFKADFKL91 MCDNAMTYNR101 PDTVYYKLAK111 KILHAGFKMM121 SKERLLALKR 131 SMS
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .4L3 or .4L32 or .4L33 or :34L3;style chemicals stick;color identity;select .A:42 or .A:43 or .A:44 or .A:45 or .A:46 or .A:47 or .A:48 or .A:49 or .A:50 or .A:53 or .A:54 or .A:57 or .A:96 or .A:99 or .A:100 or .A:106; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 5-[3,5-Dimethoxy-4-[(3-Oxidanylazetidin-1-Yl)methyl]phenyl]-1,3-Dimethyl-Pyridin-2-One | Ligand Info | |||||
| Structure Description | Crystal structure of the bromodomain of BRD9 in complex with compound 9. | PDB:5F1L | ||||
| Method | X-ray diffraction | Resolution | 2.30 Å | Mutation | No | [2] |
| PDB Sequence |
STPIQQLLEH
31 FLRQLQRKDP41 HGFFAFPVTD51 AIAPGYSMII61 KHPMDFGTMK71 DKIVANEYKS 81 VTEFKADFKL91 MCDNAMTYNR101 PDTVYYKLAK111 KILHAGFKMM121 SKERLLALKR 131 SMS
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .5U2 or .5U22 or .5U23 or :35U2;style chemicals stick;color identity;select .A:42 or .A:43 or .A:44 or .A:45 or .A:47 or .A:48 or .A:49 or .A:53 or .A:54 or .A:57 or .A:96 or .A:99 or .A:100 or .A:106; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 3-(6-acetylpyrrolo[1,2-a]pyrimidin-8-yl)-N-cyclobutyl-4-methoxybenzamide | Ligand Info | |||||
| Structure Description | Structure of the BRD9 bromodomain and compound 27 | PDB:6Y7K | ||||
| Method | X-ray diffraction | Resolution | 1.20 Å | Mutation | No | [9] |
| PDB Sequence |
ESTPIQQLLE
146 HFLRQLQRKD156 PHGFFAFPVT166 DAIAPGYSMI176 IKHPMDFGTM186 KDKIVANEYK 196 SVTEFKADFK206 LMCDNAMTYN216 RPDTVYYKLA226 KKILHAGFKM236 MSKERLLALK 246 RSMS
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .OEZ or .OEZ2 or .OEZ3 or :3OEZ;style chemicals stick;color identity;select .A:158 or .A:159 or .A:160 or .A:161 or .A:163 or .A:164 or .A:165 or .A:169 or .A:170 or .A:173 or .A:212 or .A:215 or .A:216 or .A:222; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 1-(8-Pyridin-2-ylpyrrolo[1,2-a]pyrimidin-6-yl)ethanone | Ligand Info | |||||
| Structure Description | Structure of the BRD9 bromodomain and compound 2 | PDB:6Y7I | ||||
| Method | X-ray diffraction | Resolution | 1.60 Å | Mutation | No | [10] |
| PDB Sequence |
ESTPIQQLLE
146 HFLRQLQRKD156 PHGFFAFPVT166 DAIAPGYSMI176 IKHPMDFGTM186 KDKIVANEYK 196 SVTEFKADFK206 LMCDNAMTYN216 RPDTVYYKLA226 KKILHAGFKM236 MSKERLLALK 246 RSMS
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .OF8 or .OF82 or .OF83 or :3OF8;style chemicals stick;color identity;select .A:160 or .A:161 or .A:165 or .A:169 or .A:170 or .A:173 or .A:212 or .A:215 or .A:216 or .A:222; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 1-[8-(2,5-Dimethoxyphenyl)pyrrolo[1,2-a]pyrimidin-6-yl]ethanone | Ligand Info | |||||
| Structure Description | Structure of the BRD9 bromodomain and compound 15 | PDB:6Y7J | ||||
| Method | X-ray diffraction | Resolution | 1.60 Å | Mutation | No | [11] |
| PDB Sequence |
STPIQQLLEH
147 FLRQLQRKDP157 HGFFAFPVTD167 AIAPGYSMII177 KHPMDFGTMK187 DKIVANEYKS 197 VTEFKADFKL207 MCDNAMTYNR217 PDTVYYKLAK227 KILHAGFKMM237 SKERLLALKR 247 SMS
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .OF5 or .OF52 or .OF53 or :3OF5;style chemicals stick;color identity;select .A:159 or .A:160 or .A:161 or .A:163 or .A:164 or .A:165 or .A:169 or .A:170 or .A:173 or .A:212 or .A:215 or .A:216 or .A:222; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 1-(8-Phenylpyrrolo[1,2-a]pyrimidin-6-yl)ethanone | Ligand Info | |||||
| Structure Description | Structure of the BRD9 bromodomain and compound 11 | PDB:6Y7H | ||||
| Method | X-ray diffraction | Resolution | 1.80 Å | Mutation | No | [12] |
| PDB Sequence |
ESTPIQQLLE
146 HFLRQLQRKD156 PHGFFAFPVT166 DAIAPGYSMI176 IKHPMDFGTM186 KDKIVANEYK 196 SVTEFKADFK206 LMCDNAMTYN216 RPDTVYYKLA226 KKILHAGFKM236 MSKERLLALK 246 RSMS
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .OFK or .OFK2 or .OFK3 or :3OFK;style chemicals stick;color identity;select .A:160 or .A:161 or .A:165 or .A:169 or .A:170 or .A:173 or .A:212 or .A:215 or .A:216 or .A:222; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: N-[6-({2-[(3s)-2,6-Dioxopiperidin-3-Yl]-1,3-Dioxo-2,3-Dihydro-1h-Isoindol-4-Yl}oxy)hexyl]-2-(4-{2-[n-(1,1-Dioxo-1lambda~6~-Thian-4-Yl)carbamimidoyl]-5-Methyl-4-Oxo-4,5-Dihydrothieno[3,2-C]pyridin-7-Yl}-2-Methoxyphenoxy)acetamide | Ligand Info | |||||
| Structure Description | Crystal Structure of BRD9 bromodomain | PDB:5TWX | ||||
| Method | X-ray diffraction | Resolution | 2.55 Å | Mutation | No | [13] |
| PDB Sequence |
ESTPIQQLLE
146 HFLRQLQRKD156 PHGFFAFPVT166 DAIAPGYSMI176 IKHPMDFGTM186 KDKIVANEYK 196 SVTEFKADFK206 LMCDNAMTYN216 RPDTVYYKLA226 KKILHAGFKM236 MSKQAALLGN 246 EDTA
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .7P7 or .7P72 or .7P73 or :37P7;style chemicals stick;color identity;select .A:160 or .A:161 or .A:165 or .A:169 or .A:170 or .A:171 or .A:173 or .A:212 or .A:215 or .A:216 or .A:217 or .A:220 or .A:222; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: N-(1,1-dioxothian-4-yl)-7-[3-methyl-1-(piperidin-4-ylmethyl)indol-5-yl]-4-oxo-5-propylthieno[3,2-c]pyridine-2-carboxamide | Ligand Info | |||||
| Structure Description | Crystal structure of BRD9 bromodomain in complex with compound EA-89 | PDB:8A7I | ||||
| Method | X-ray diffraction | Resolution | 1.76 Å | Mutation | No | [14] |
| PDB Sequence |
STPIQQLLEH
147 FLRQLQRKDP157 HGFFAFPVTD167 AIAPGYSMII177 KHPMDFGTMK187 DKIVANEYKS 197 VTEFKADFKL207 MCDNAMTYNR217 PDTVYYKLAK227 KILHAGFKMM237 S |
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .L8L or .L8L2 or .L8L3 or :3L8L;style chemicals stick;color identity;select .A:158 or .A:159 or .A:160 or .A:161 or .A:163 or .A:165 or .A:169 or .A:170 or .A:173 or .A:212 or .A:215 or .A:216 or .A:217 or .A:220 or .A:222; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 2-Amino-1,3-benzothiazole-6-carboxamide | Ligand Info | |||||
| Structure Description | Crystal structure of the BRD9 bromodomain and hit 1 | PDB:5JI8 | ||||
| Method | X-ray diffraction | Resolution | 1.42 Å | Mutation | No | [15] |
| PDB Sequence |
TPIQQLLEHF
148 LRQLQRKDPH158 GFFAFPVTDA168 IAPGYSMIIK178 HPMDFGTMKD188 KIVANEYKSV 198 TEFKADFKLM208 CDNAMTYNRP218 DTVYYKLAKK228 ILHAGFKMMS238 |
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .6KT or .6KT2 or .6KT3 or :36KT;style chemicals stick;color identity;select .A:160 or .A:161 or .A:165 or .A:169 or .A:170 or .A:173 or .A:208 or .A:212 or .A:215 or .A:216 or .A:222; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 7-(3,4-Dimethoxyphenyl)-5-Methyl-2-(4-Methylsulfonylpiperazin-1-Yl)carbonyl-Thieno[3,2-C]pyridin-4-One | Ligand Info | |||||
| Structure Description | BROMODOMAIN OF HUMAN BRD9 WITH 7-(3,4-dimethoxyphenyl)-2-(4- methanesulfonylpiperazine-1-carbonyl)-5-methyl-4H,5H-thieno-3,2-c- pyridin-4-one | PDB:4UIT | ||||
| Method | X-ray diffraction | Resolution | 1.30 Å | Mutation | No | [16] |
| PDB Sequence |
STPIQQLLEH
31 FLRQLQRKDP41 HGFFAFPVTD51 AIAPGYSMII61 KHPMDFGTMK71 DKIVANEYKS 81 VTEFKADFKL91 MCDNAMTYNR101 PDTVYYKLAK111 KILHAGFKMM121 S |
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .N1D or .N1D2 or .N1D3 or :3N1D;style chemicals stick;color identity;select .A:43 or .A:44 or .A:45 or .A:49 or .A:53 or .A:54 or .A:55 or .A:57 or .A:96 or .A:99 or .A:100 or .A:101 or .A:104 or .A:106; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 4-Chloro-2-methyl-5-(methylamino)pyridazin-3(2H)-one | Ligand Info | |||||
| Structure Description | BRD9 with 4-chloro-2-methyl-methylamino-pyridazinone | PDB:6YQW | ||||
| Method | X-ray diffraction | Resolution | 1.50 Å | Mutation | No | [17] |
| PDB Sequence |
STPIQQLLEH
31 FLRQLQRKDP41 HGFFAFPVTD51 AIAPGYSMII61 KHPMDFGTMK71 DKIVANEYKS 81 VTEFKADFKL91 MCDNAMTYNR101 PDTVYYKLAK111 KILHAGFKMM121 S |
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .82I or .82I2 or .82I3 or :382I;style chemicals stick;color identity;select .A:44 or .A:45 or .A:49 or .A:53 or .A:54 or .A:57 or .A:96 or .A:99 or .A:100 or .A:106; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: N-[1,1-Bis(Oxidanylidene)thian-4-Yl]-7-(3,4-Dimethoxyphenyl)-5-Methyl-4-Oxidanylidene-Thieno[3,2-C]pyridine-2-Carboxamide | Ligand Info | |||||
| Structure Description | BROMODOMAIN OF HUMAN BRD9 WITH 7-(3,4-dimethoxyphenyl)-N-(1,1-dioxo-1- thian-4-yl)-5-methyl-4-oxo-4H,5H-thieno-3,2-c-pyridine-2-carboxamide | PDB:4UIU | ||||
| Method | X-ray diffraction | Resolution | 1.64 Å | Mutation | No | [16] |
| PDB Sequence |
STPIQQLLEH
31 FLRQLQRKDP41 HGFFAFPVTD51 AIAPGYSMII61 KHPMDFGTMK71 DKIVANEYKS 81 VTEFKADFKL91 MCDNAMTYNR101 PDTVYYKLAK111 KILHAGFKMM121 S |
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .TVU or .TVU2 or .TVU3 or :3TVU;style chemicals stick;color identity;select .A:43 or .A:44 or .A:45 or .A:46 or .A:47 or .A:48 or .A:49 or .A:53 or .A:54 or .A:57 or .A:96 or .A:99 or .A:100 or .A:101 or .A:104 or .A:106; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 4-chloranyl-2-methyl-5-[(2-methyl-3,4-dihydro-1~{H}-isoquinolin-5-yl)amino]pyridazin-3-one | Ligand Info | |||||
| Structure Description | BROMODOMAIN OF HUMAN BRD9 WITH 4-chloro-2-methyl-5-((2-methyl-1,2,3,4-tetrahydroisoquinolin-5-yl)amino)pyridazin-3(2H)-one | PDB:5MKY | ||||
| Method | X-ray diffraction | Resolution | 1.67 Å | Mutation | No | [18] |
| PDB Sequence |
STPIQQLLEH
31 FLRQLQRKDP41 HGFFAFPVTD51 AIAPGYSMII61 KHPMDFGTMK71 DKIVANEYKS 81 VTEFKADFKL91 MCDNAMTYNR101 PDTVYYKLAK111 KILHAGFKMM121 S |
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .I0D or .I0D2 or .I0D3 or :3I0D;style chemicals stick;color identity;select .A:28 or .A:31 or .A:32 or .A:43 or .A:44 or .A:45 or .A:47 or .A:48 or .A:49 or .A:53 or .A:54 or .A:57 or .A:82 or .A:96 or .A:99 or .A:100 or .A:106 or .A:121 or .A:122; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: N-[1,1-Bis(Oxidanylidene)thian-4-Yl]-5-Methyl-4-Oxidanylidene-7-[3-(Trifluoromethyl)phenyl]thieno[3,2-C]pyridine-2-Carboximidamide | Ligand Info | |||||
| Structure Description | BROMODOMAIN OF HUMAN BRD9 WITH N-(1,1-dioxo-1-thian-4-yl)-5-methyl-4- oxo-7-3-(trifluoromethyl)phenyl-4H,5H-thieno-3,2-c-pyridine-2- carboximidamide | PDB:4UIV | ||||
| Method | X-ray diffraction | Resolution | 1.72 Å | Mutation | No | [16] |
| PDB Sequence |
STPIQQLLEH
31 FLRQLQRKDP41 HGFFAFPVTD51 AIAPGYSMII61 KHPMDFGTMK71 DKIVANEYKS 81 VTEFKADFKL91 MCDNAMTYNR101 PDTVYYKLAK111 KILHAGFKMM121 S |
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .XZB or .XZB2 or .XZB3 or :3XZB;style chemicals stick;color identity;select .A:43 or .A:44 or .A:45 or .A:49 or .A:53 or .A:54 or .A:55 or .A:57 or .A:96 or .A:99 or .A:100 or .A:101 or .A:104 or .A:106; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 3-[6-(But-3-En-1-Yl)-7-Oxo-6,7-Dihydro-1h-Pyrrolo[2,3-C]pyridin-4-Yl]-N,N-Dimethylbenzamide | Ligand Info | |||||
| Structure Description | BRD9 bromodomain in complex with 3-(6-(but-3-en-1-yl)-7-oxo-6,7-dihydro-1H-pyrrolo[2,3-c]pyridin-4-yl)-N,N-dimethylbenzamide | PDB:6BQA | ||||
| Method | X-ray diffraction | Resolution | 1.03 Å | Mutation | No | [19] |
| PDB Sequence |
STPIQQLLEH
31 FLRQLQRKDP41 HGFFAFPVTD51 AIAPGYSMII61 KHPMDFGTMK71 DKIVANEYKS 81 VTEFKADFKL91 MCDNAMTYNR101 PDTVYYKLAK111 KILHAGFKMM121 SK |
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .67C or .67C2 or .67C3 or :367C;style chemicals stick;color identity;select .A:40 or .A:44 or .A:45 or .A:47 or .A:48 or .A:49 or .A:53 or .A:54 or .A:57 or .A:92 or .A:96 or .A:99 or .A:100 or .A:105 or .A:106 or .A:107 or .A:109 or .A:110; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 6-methyl-1,6-dihydro-7H-pyrrolo[2,3-c]pyridin-7-one | Ligand Info | |||||
| Structure Description | BRD9 in complex with Cpd1 (6-methyl-1,6-dihydro-7H-pyrrolo[2,3-c]pyridin-7-one) | PDB:5I40 | ||||
| Method | X-ray diffraction | Resolution | 1.04 Å | Mutation | No | [20] |
| PDB Sequence |
STPIQQLLEH
31 FLRQLQRKDP41 HGFFAFPVTD51 AIAPGYSMII61 KHPMDFGTMK71 DKIVANEYKS 81 VTEFKADFKL91 MCDNAMTYNR101 PDTVYYKLAK111 KILHAGFKMM121 SK |
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .67N or .67N2 or .67N3 or :367N;style chemicals stick;color identity;select .A:44 or .A:45 or .A:49 or .A:53 or .A:54 or .A:57 or .A:96 or .A:99 or .A:100 or .A:106; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: N,N-Dimethyl-3-(6-Methyl-7-Oxo-6,7-Dihydro-1h-Pyrrolo[2,3-C]pyridin-4-Yl)benzamide | Ligand Info | |||||
| Structure Description | BRD9 in complex with Cpd2 (N,N-dimethyl-3-(6-methyl-7-oxo-6,7-dihydro-1H-pyrrolo[2,3-c]pyridin-4-yl)benzamide) | PDB:5I7X | ||||
| Method | X-ray diffraction | Resolution | 1.18 Å | Mutation | No | [20] |
| PDB Sequence |
STPIQQLLEH
31 FLRQLQRKDP41 HGFFAFPVTD51 AIAPGYSMII61 KHPMDFGTMK71 DKIVANEYKS 81 VTEFKADFKL91 MCDNAMTYNR101 PDTVYYKLAK111 KILHAGFKMM121 S |
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .67B or .67B2 or .67B3 or :367B;style chemicals stick;color identity;select .A:44 or .A:45 or .A:49 or .A:53 or .A:54 or .A:57 or .A:96 or .A:99 or .A:100 or .A:106; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 3-{6-[(2e)-But-2-En-1-Yl]-7-Oxo-6,7-Dihydro-1h-Pyrrolo[2,3-C]pyridin-4-Yl}-N,N-Dimethylbenzamide | Ligand Info | |||||
| Structure Description | BRD9 in complex with Cpd4 ((E)-3-(6-(but-2-en-1-yl)-7-oxo-6,7-dihydro-1H-pyrrolo[2,3-c]pyridin-4-yl)-N,N-dimethylbenzamide) | PDB:5I7Y | ||||
| Method | X-ray diffraction | Resolution | 1.45 Å | Mutation | No | [20] |
| PDB Sequence |
STPIQQLLEH
31 FLRQLQRKDP41 HGFFAFPVTD51 AIAPGYSMII61 KHPMDFGTMK71 DKIVANEYKS 81 VTEFKADFKL91 MCDNAMTYNR101 PDTVYYKLAK111 KILHAGFKMM121 S |
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .69G or .69G2 or .69G3 or :369G;style chemicals stick;color identity;select .A:44 or .A:45 or .A:49 or .A:53 or .A:54 or .A:57 or .A:96 or .A:99 or .A:100 or .A:106 or .A:109 or .A:110; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: (2~{S},4~{S})-1-[(2~{S})-2-[2-[2-[2-[4-[[2,6-dimethoxy-4-(2-methyl-1-oxidanylidene-2,7-naphthyridin-4-yl)phenyl]methyl]piperazin-1-yl]ethoxy]ethoxy]ethanoylamino]-3,3-dimethyl-butanoyl]-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide | Ligand Info | |||||
| Structure Description | Crystal structure of human BRD9 bromodomain in complex with a PROTAC | PDB:6HM0 | ||||
| Method | X-ray diffraction | Resolution | 2.40 Å | Mutation | No | [21] |
| PDB Sequence |
STPIQQLLEH
31 FLRQLQRKDP41 HGFFAFPVTD51 AIAPGYSMII61 KHPMDFGTMK71 DKIVANEYKS 81 VTEFKADFKL91 MCDNAMTYNR101 PDTVYYKLAK111 KILHAGFKMM121 SKERLLALKR 131 SM
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .GBW or .GBW2 or .GBW3 or :3GBW;style chemicals stick;color identity;select .A:41 or .A:42 or .A:43 or .A:44 or .A:45 or .A:46 or .A:47 or .A:48 or .A:49 or .A:53 or .A:54 or .A:57 or .A:96 or .A:99 or .A:100 or .A:106; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | Structural Basis of Inhibitor Selectivity in the BRD7/9 Subfamily of Bromodomains. J Med Chem. 2020 Mar 26;63(6):3227-3237. | ||||
| REF 2 | Structure-Based Design of an in Vivo Active Selective BRD9 Inhibitor. J Med Chem. 2016 May 26;59(10):4462-75. | ||||
| REF 3 | Promiscuous targeting of bromodomains by bromosporine identifies BET proteins as master regulators of primary transcription response in leukemia. Sci Adv. 2016 Oct 12;2(10):e1600760. | ||||
| REF 4 | Crystal structure of BRD9 bromodomain in complex with LP99 chemical probe | ||||
| REF 5 | 9H-purine scaffold reveals induced-fit pocket plasticity of the BRD9 bromodomain. J Med Chem. 2015 Mar 26;58(6):2718-36. | ||||
| REF 6 | Crystal Structure of the bromodomain of human BRD9 in complex with a triazolo-phthalazine ligand | ||||
| REF 7 | LP99: Discovery and Synthesis of the First Selective BRD7/9 Bromodomain Inhibitor. Angew Chem Int Ed Engl. 2015 May 18;54(21):6217-21. | ||||
| REF 8 | Crystal structure of BRD9 bromodomain in complex with an indolizine ligand | ||||
| REF 9 | Structure of the BRD9 bromodomain | ||||
| REF 10 | Structure of the BRD9 bromodomain and compound 2 | ||||
| REF 11 | Structure of the BRD9 bromodomain | ||||
| REF 12 | Structure of the BRD9 bromodomain | ||||
| REF 13 | Degradation of the BAF Complex Factor BRD9 by Heterobifunctional Ligands. Angew Chem Int Ed Engl. 2017 May 15;56(21):5738-5743. | ||||
| REF 14 | BRD9 degraders as chemosensitizers in acute leukemia and multiple myeloma. Blood Cancer J. 2022 Jul 19;12(7):110. | ||||
| REF 15 | NMR Fragment Screening Hit Induces Plasticity of BRD7/9 Bromodomains. Chembiochem. 2016 Aug 3;17(15):1456-63. | ||||
| REF 16 | Discovery of I-BRD9, a Selective Cell Active Chemical Probe for Bromodomain Containing Protein 9 Inhibition. J Med Chem. 2016 Feb 25;59(4):1425-39. | ||||
| REF 17 | Application of Atypical Acetyl-lysine Methyl Mimetics in the Development of Selective Inhibitors of the Bromodomain-Containing Protein 7 (BRD7)/Bromodomain-Containing Protein 9 (BRD9) Bromodomains. J Med Chem. 2020 Jun 11;63(11):5816-5840. | ||||
| REF 18 | Discovery of a Potent, Cell Penetrant, and Selective p300/CBP-Associated Factor (PCAF)/General Control Nonderepressible 5 (GCN5) Bromodomain Chemical Probe. J Med Chem. 2017 Jan 26;60(2):695-709. | ||||
| REF 19 | Water molecules in protein-ligand interfaces. Evaluation of software tools and SAR comparison. J Comput Aided Mol Des. 2019 Mar;33(3):307-330. | ||||
| REF 20 | Diving into the Water: Inducible Binding Conformations for BRD4, TAF1(2), BRD9, and CECR2 Bromodomains. J Med Chem. 2016 Jun 9;59(11):5391-402. | ||||
| REF 21 | Iterative Design and Optimization of Initially Inactive Proteolysis Targeting Chimeras (PROTACs) Identify VZ185 as a Potent, Fast, and Selective von Hippel-Lindau (VHL) Based Dual Degrader Probe of BRD9 and BRD7. J Med Chem. 2019 Jan 24;62(2):699-726. | ||||
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