Binding Site Information of Target
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T24823 | Target Info | |||
| Target Name | Lysine-specific histone demethylase 1B (KDM1B) | ||||
| Synonyms | Lysine-specific histone demethylase 2; LSD2; Flavin-containing amine oxidase domain-containing protein 1; C6orf193; AOF1 | ||||
| Target Type | Patented-recorded Target | ||||
| Gene Name | KDM1B | ||||
| Biochemical Class | CH-NH(2) donor oxidoreductase | ||||
| UniProt ID | |||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| Ligand Name: Flavin-Adenine Dinucleotide | Ligand Info | |||||
| Structure Description | Crystal structure of LSD2-NPAC with H3(1-26)in space group P21 | PDB:4HSU | ||||
| Method | X-ray diffraction | Resolution | 1.99 Å | Mutation | Yes | [1] |
| PDB Sequence |
GSRKCEKAGC
58 TATCPVCFAS68 ASERCAKNGY78 TSRWYHLSCG88 EHFCNECFDH98 YYRSHKDGYD 108 KYTTWKKIWT118 SNGKTEPSPK128 AFMADQQLPY138 WVQCTKPECR148 KWRQLTKEIQ 158 LTPQIAKTYR168 CGMKSDHCSL187 PEDLRVLEVS197 NHWWYSMLIL207 PPLLKDSVAA 217 PLLSAYYPDC227 VGMSPSCTGM265 NRYFQPFYQP275 NECGKALCVR285 PDVMELDELY 295 EFPEYSRDPT305 MYLALRNLIL315 ALWYTNCKEA325 LTPQKCIPHI335 IVRGLVRIRC 345 VQEVERILYF355 MTRKGLINTG365 VLSVGADQYL375 LPKDYHNKSV385 IIIGAGPAGL 395 AAARQLHNFG405 IKVTVLEAKD415 RIGGRVWDDK425 SFKGVTVGRG435 AQIVNGCINN 445 PVALMCEQLG455 ISMHKFGERC465 DLIQEGGRIT475 DPTIDKRMDF485 HFNALLDVVS 495 EWRKDKTQLQ505 DVPLGEKIEE515 IYKAFIKESG525 IQFSELEGQV535 LQFHLSNLEY 545 ACGSNLHQVS555 ARSWDHNEFF565 AQFAGDHTLL575 TPGYSVIIEK585 LAEGLDIQLK 595 SPVQCIDYSG605 DEVQVTTTDG615 TGYSAQKVLV625 TVPLALLQKG635 AIQFNPPLSE 645 KKMKAINSLG655 AGIIEKIALQ665 FPYRFWDSKV675 QGADFFGHVP685 PSASKRGLFA 695 VFYDMDPQKK705 HSVLMSVIAG715 EAVASVRTLD725 DKQVLQQCMA735 TLRELFKEQE 745 VPDPTKYFVT755 RWSTDPWIQM765 AYSFVKTGGS775 GEAYDIIAED785 IQGTVFFAGE 795 ATNRHFPQTV805 TGAYLSGVRE815 ASKIAAF
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ILE388
3.605
GLY389
3.374
ALA390
3.787
GLY391
3.608
PRO392
3.243
ALA393
2.901
GLY394
4.476
LEU411
3.381
GLU412
2.267
ALA413
3.146
LYS414
3.266
ARG416
4.954
GLY418
3.869
GLY419
3.556
ARG420
2.700
VAL421
4.304
ARG434
3.513
GLY435
3.583
ALA436
3.250
GLN437
3.707
ILE438
3.068
ASN440
4.049
TYR545
4.915
TYR579
3.898
SER596
4.084
PRO597
3.743
VAL598
3.143
THR626
3.815
VAL627
3.399
PRO628
3.550
LEU631
4.294
ILE637
4.204
ILE659
3.864
LYS661
4.088
TRP757
3.532
TRP762
3.228
ILE763
4.289
MET765
4.078
ALA766
3.602
TYR767
3.732
GLY794
3.294
GLU795
3.299
GLN803
2.372
THR804
3.443
VAL805
3.044
THR806
4.726
ALA808
3.232
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: 3-(4-Bromophenyl)propanal | Ligand Info | |||||
| Structure Description | Crystal structure of LSD2 in complex with trans-4-Br-PCPA | PDB:7XE2 | ||||
| Method | X-ray diffraction | Resolution | 2.05 Å | Mutation | No | [2] |
| PDB Sequence |
EKKYRKCEKA
56 GCTATCPVCF66 ASASERCAKN76 GYTSRWYHLS86 CGEHFCNECF96 DHYYRSHKDG 106 YDKYTTWKKI116 WTSNGKTEPS126 PKAFMADQQL136 PYWVQCTKPE146 CRKWRQLTKE 156 IQLTPQIAKT166 YRCGMKPNTE180 TSDHCSLPED190 LRVLEVSNHW200 WYSMLILPPL 210 LKDSVAAPLL220 SAYYPDCVGM230 SPSCTSTNRH261 VPGMNRYFQP271 FYQPNECGKA 281 LCVRPDVMEL291 DELYEFPEYS301 RDPTMYLALR311 NLILALWYTN321 CKEALTPQKC 331 IPHIIVRGLV341 RIRCVQEVER351 ILYFMTRKGL361 INTGVLSVGA371 DQYLLPKDYH 381 NKSVIIIGAG391 PAGLAAARQL401 HNFGIKVTVL411 EAKDRIGGRV421 WDDKSFKGVT 431 VGRGAQIVNG441 CINNPVALMC451 EQLGISMHKF461 GERCDLIQEG471 GRITDPTIDK 481 RMDFHFNALL491 DVVSEWRKDK501 TQLQDVPLGE511 KIEEIYKAFI521 KESGIQFSEL 531 EGQVLQFHLS541 NLEYACGSNL551 HQVSARSWDH561 NEFFAQFAGD571 HTLLTPGYSV 581 IIEKLAEGLD591 IQLKSPVQCI601 DYSGDEVQVT611 TTDGTGYSAQ621 KVLVTVPLAL 631 LQKGAIQFNP641 PLSEKKMKAI651 NSLGAGIIEK661 IALQFPYRFW671 DSKVQGADFF 681 GHVPPSASKR691 GLFAVFYDMD701 PQKKHSVLMS711 VIAGEAVASV721 RTLDDKQVLQ 731 QCMATLRELF741 KEQEVPDPTK751 YFVTRWSTDP761 WIQMAYSFVK771 TGGSGEAYDI 781 IAEDIQGTVF791 FAGEATNRHF801 PQTVTGAYLS811 GVREASKIAA821 F |
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: 3-(4-Bromo-2,5-difluorophenyl)propanal | Ligand Info | |||||
| Structure Description | Crystal structure of LSD2 in complex with cis-4-Br-2,5-F2-PCPA (S1024) | PDB:7XE3 | ||||
| Method | X-ray diffraction | Resolution | 2.82 Å | Mutation | No | [2] |
| PDB Sequence |
SEKKYRKCEK
55 AGCTATCPVC65 FASASERCAK75 NGYTSRWYHL85 SCGEHFCNEC95 FDHYYRSHKD 105 GYDKYTTWKK115 IWTSNGKTEP125 SPKAFMADQQ135 LPYWVQCTKP145 ECRKWRQLTK 155 EIQLTPQIAK165 TYRCGMKPNT175 TSDHCSLPED190 LRVLEVSNHW200 WYSMLILPPL 210 LKDSVAAPLL220 SAYYPDCVGM230 SPSCTSVPGM265 NRYFQPFYQP275 NECGKALCVR 285 PDVMELDELY295 EFPEYSRDPT305 MYLALRNLIL315 ALWYTNCKEA325 LTPQKCIPHI 335 IVRGLVRIRC345 VQEVERILYF355 MTRKGLINTG365 VLSVGADQYL375 LPKDYHNKSV 385 IIIGAGPAGL395 AAARQLHNFG405 IKVTVLEAKD415 RIGGRVWDDK425 SFKGVTVGRG 435 AQIVNGCINN445 PVALMCEQLG455 ISMHKFGERC465 DLIQEGGRIT475 DPTIDKRMDF 485 HFNALLDVVS495 EWRKDKTQLQ505 DVPLGEKIEE515 IYKAFIKESG525 IQFSELEGQV 535 LQFHLSNLEY545 ACGSNLHQVS555 ARSWDHNEFF565 AQFAGDHTLL575 TPGYSVIIEK 585 LAEGLDIQLK595 SPVQCIDYSG605 DEVQVTTTDG615 TGYSAQKVLV625 TVPLALLQKG 635 AIQFNPPLSE645 KKMKAINSLG655 AGIIEKIALQ665 FPYRFWDSKV675 QGADFFGHVP 685 PSASKRGLFA695 VFYDMDPQKK705 HSVLMSVIAG715 EAVASVRTLD725 DKQVLQQCMA 735 TLRELFKEQE745 VPDPTKYFVT755 RWSTDPWIQM765 AYSFVKTGGS775 GEAYDIIAED 785 IQGTVFFAGE795 ATNRHFPQTV805 TGAYLSGVRE815 ASKIAAF
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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 .8A2 or .8A22 or .8A23 or :38A2;style chemicals stick;color identity;select .A:435 or .A:436 or .A:437 or .A:438 or .A:439 or .A:440 or .A:545 or .A:546 or .A:659 or .A:661 or .A:767 or .A:803 or .A:804; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4S)-5-[(3R,3as,7ar)-10,11-dimethyl-1,4,6-trioxo-3-phenyl-2,3,5,6,7,7a-hexahydro-1H-benzo[g]pyrrolo[2,1-E]pteridin-8(4H)-yl]-2,3,4-trihydroxypentyl dihydrogen dip | Ligand Info | |||||
| Structure Description | Crystal structure of LSD2-NPAC with tranylcypromine | PDB:4GUU | ||||
| Method | X-ray diffraction | Resolution | 2.30 Å | Mutation | No | [3] |
| PDB Sequence |
PLGSRKCEKA
56 GCTATCPVCF66 ASASERCAKN76 GYTSRWYHLS86 CGEHFCNECF96 DHYYRSHKDG 106 YDKYTTWKKI116 WTSNGKTEPS126 PKAFMADQQL136 PYWVQCTKPE146 CRKWRQLTKE 156 IQLTPQIAKT166 YRCGMKPNSD183 HCSLPEDLRV193 LEVSNHWWYS203 MLILPPLLKD 213 SVAAPLLSAY223 YPDCVGMSPS233 CTGMNRYFQP271 FYQPNECGKA281 LCVRPDVMEL 291 DELYEFPEYS301 RDPTMYLALR311 NLILALWYTN321 CKEALTPQKC331 IPHIIVRGLV 341 RIRCVQEVER351 ILYFMTRKGL361 INTGVLSVGA371 DQYLLPKDYH381 NKSVIIIGAG 391 PAGLAAARQL401 HNFGIKVTVL411 EAKDRIGGRV421 WDDKSFKGVT431 VGRGAQIVNG 441 CINNPVALMC451 EQLGISMHKF461 GERCDLIQEG471 GRITDPTIDK481 RMDFHFNALL 491 DVVSEWRKDK501 TQLQDVPLGE511 KIEEIYKAFI521 KESGIQFSEL531 EGQVLQFHLS 541 NLEYACGSNL551 HQVSARSWDH561 NEFFAQFAGD571 HTLLTPGYSV581 IIEKLAEGLD 591 IQLKSPVQCI601 DYSGDEVQVT611 TTDGTGYSAQ621 KVLVTVPLAL631 LQKGAIQFNP 641 PLSEKKMKAI651 NSLGAGIIEK661 IALQFPYRFW671 DSKVQGADFF681 GHVPPSASKR 691 GLFAVFYDMD701 PQKKHSVLMS711 VIAGEAVASV721 RTLDDKQVLQ731 QCMATLRELF 741 KEQEVPDPTK751 YFVTRWSTDP761 WIQMAYSFVK771 TGGSGEAYDI781 IAEDIQGTVF 791 FAGEATNRHF801 PQTVTGAYLS811 GVREASKIAA821
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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 .FA9 or .FA92 or .FA93 or :3FA9;style chemicals stick;color identity;select .A:388 or .A:389 or .A:390 or .A:391 or .A:392 or .A:393 or .A:394 or .A:411 or .A:412 or .A:413 or .A:414 or .A:418 or .A:419 or .A:420 or .A:421 or .A:434 or .A:435 or .A:436 or .A:437 or .A:438 or .A:439 or .A:440 or .A:545 or .A:546 or .A:579 or .A:596 or .A:597 or .A:598 or .A:626 or .A:627 or .A:628 or .A:631 or .A:637 or .A:659 or .A:661 or .A:757 or .A:762 or .A:763 or .A:765 or .A:766 or .A:767 or .A:794 or .A:795 or .A:803 or .A:804 or .A:805 or .A:806 or .A:808; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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ILE388
3.465
GLY389
3.397
ALA390
4.112
GLY391
3.550
PRO392
3.446
ALA393
2.970
GLY394
4.541
LEU411
3.374
GLU412
2.564
ALA413
3.145
LYS414
3.427
GLY418
3.699
GLY419
3.179
ARG420
2.767
VAL421
4.113
ARG434
3.834
GLY435
3.719
ALA436
3.242
GLN437
2.854
ILE438
2.829
VAL439
5.000
ASN440
4.264
TYR545
3.081
ALA546
3.873
TYR579
3.956
SER596
4.060
PRO597
3.756
VAL598
3.000
THR626
3.584
VAL627
3.194
PRO628
3.547
LEU631
4.160
ILE637
3.771
ILE659
3.725
LYS661
3.765
TRP757
3.677
TRP762
3.295
ILE763
4.326
MET765
4.367
ALA766
3.673
TYR767
3.174
GLY794
3.271
GLU795
3.109
GLN803
2.483
THR804
3.477
VAL805
3.064
THR806
4.688
ALA808
3.433
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| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | Structural insight into substrate recognition by histone demethylase LSD2/KDM1b. Cell Res. 2013 Feb;23(2):306-9. | ||||
| REF 2 | Structure-Activity Relationship and In Silico Evaluation of cis- and trans-PCPA-Derived Inhibitors of LSD1 and LSD2. doi:10.1021/acsmedchemlett.2c00294. | ||||
| REF 3 | LSD2/KDM1B and its cofactor NPAC/GLYR1 endow a structural and molecular model for regulation of H3K4 demethylation. Mol Cell. 2013 Feb 7;49(3):558-70. | ||||
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