Target Binding Site Detail

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Target General Information
Ligand General Information
Drug Binding Sites of Target
References
Target General Information  Top
Target ID T32880 Target Info
Target Name HIF-prolyl hydroxylase 2 (HPH-2)
Synonyms SM-20; Prolyl hydroxylase domain-containing protein 2; PHD2; Hypoxia-inducible factor prolyl hydroxylase 2; HPH-2; HIF-PH2; Egl nine homolog 1; C1orf12
Target Type Patented-recorded Target
Gene Name EGLN1
Biochemical Class Paired donor oxygen oxidoreductase
UniProt ID
EGLN1_HUMAN
Ligand General Information  Top
Ligand Name 2-(carboxymethylamino)-2-oxoacetic acid Ligand Info
Canonical SMILES C(C(=O)O)NC(=O)C(=O)O
InChI 1S/C4H5NO5/c6-2(7)1-5-3(8)4(9)10/h1H2,(H,5,8)(H,6,7)(H,9,10)
InChIKey BIMZLRFONYSTPT-UHFFFAOYSA-N
PubChem Compound ID 3080614
Drug Binding Sites of Target  Top
PDB ID: 5L9R      HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with N-oxalylglycine (NOG)
Method X-ray diffraction Resolution 1.81 Å Mutation Yes [1]
PDB Sequence
TKPLPALKLA
194
LEYIVPAMNK
204
HGICVVDDFL
214
GKETGQQIGD
224
EVRALHDTGK
234

FTDGQLVSQK
244
SDSSKDIRGD
254
KITWIEGKEP
264
GCETIGLLMS
274
SMDDLIRHCN
284

GKLGSYKING
294
RTKAMVACYP
304
GNGTGYVRHV
314
DNPNGDGRCV
324
TCIYYLNKDW
334

DAKVSGGILR
344
IFPEGKAQFA
354
DIEPKFDRLL
364
FFWSDRRNPH
374
EVQPAYATRY
384

AITVWYFDAD
394
ERAAAKVKYL
404
Residue
Distance (Å)
ILE207
3.960
VAL209
2.340
ASP211
4.865
ARG252
3.918
ASP254
4.467
MET299
2.470
TYR303
2.750
TYR310
2.859
HIS313
2.722
ASP315
3.366
ILE327
2.505
TYR329
1.766
LEU343
2.301
ALA354
2.586
Residue
Distance (Å)
ASP355
2.413
ILE356
2.087
GLU357
4.059
PRO358
4.853
ARG362
2.924
LEU364
4.973
PHE366
4.314
HIS374
2.646
VAL376
2.511
ARG383
1.868
ALA385
3.586
THR387
4.421
TRP389
3.414
PDB ID: 5L9V      HIF prolyl hydroxylase 2 (PHD2-R281C/P317C) cross-linked to HIF-1alpha NODD-L397C/D412C and N-oxalylglycine (NOG) (complex-1)
Method X-ray diffraction Resolution 1.83 Å Mutation Yes [1]
PDB Sequence
PALKLALEYI
198
VPAMNKHGIC
208
VVDDFLGKET
218
GQQIGDEVRA
228
LHDTGKFTDG
238

QLVSQKSDSS
248
KDIRGDKITW
258
IEGKEPGCET
268
IGLLMSSMDD
278
LICHCNGKLG
288

SYKINGRTKA
298
MVACYPGNGT
308
GYVRHVDNCN
318
GDGRCVTCIY
328
YLNKDWDAKV
338

SGGILRIFPE
348
GKAQFADIEP
358
KFDRLLFFWS
368
DRRNPHEVQP
378
AYATRYAITV
388

WYFDADERAA
398
AKVKY
Residue
Distance (Å)
ARG252
3.904
ASP254
4.489
MET299
2.579
TYR303
3.310
TYR310
2.812
HIS313
2.655
ASP315
3.533
ILE327
2.619
TYR329
1.870
LEU343
2.258
Residue
Distance (Å)
PRO358
4.774
LEU364
4.940
PHE366
4.256
HIS374
2.429
GLU375
4.948
VAL376
2.432
ARG383
2.072
ALA385
3.897
THR387
4.860
TRP389
3.148
PDB ID: 5LAS      HIF prolyl hydroxylase 2 (PHD2-R281C/P317C/R396T) cross-linked to HIF-1alpha NODD-L397C/D412C and N-oxalylglycine (NOG) (complex-3)
Method X-ray diffraction Resolution 2.10 Å Mutation Yes [1]
PDB Sequence
PALKLALEYI
198
VPAMNKHGIC
208
VVDDFLGKET
218
GQQIGDEVRA
228
LHDTGKFTDG
238

QLVSQKSDSS
248
KDIRGDKITW
258
IEGKEPGCET
268
IGLLMSSMDD
278
LICHCNGKLG
288

SYKINGRTKA
298
MVACYPGNGT
308
GYVRHVDNCN
318
GDGRCVTCIY
328
YLNKDWDAKV
338

SGGILRIFPE
348
GKAQFADIEP
358
KFDRLLFFWS
368
DRRNPHEVQP
378
AYATRYAITV
388

WYFDADETAA
398
AKVKY
Residue
Distance (Å)
ARG252
3.840
ASP254
4.628
MET299
2.584
TYR303
3.397
TYR310
2.829
HIS313
2.395
ASP315
3.427
ILE327
2.661
TYR329
1.924
LEU343
2.188
Residue
Distance (Å)
PRO358
4.939
LEU364
4.825
PHE366
4.299
HIS374
2.486
GLU375
4.997
VAL376
2.367
ARG383
2.045
ALA385
3.843
THR387
4.699
TRP389
3.224
PDB ID: 5LA9      HIF prolyl hydroxylase 2 (PHD2-R281C/V314C) cross-linked to HIF-1alpha NODD-L397C/D412C and N-oxalylglycine (NOG) (complex-2)
Method X-ray diffraction Resolution 2.81 Å Mutation Yes [1]
PDB Sequence
LPALKLALEY
197
IVPAMNKHGI
207
CVVDDFLGKE
217
TGQQIGDEVR
227
ALHDTGKFTD
237

GQLVIRGDKI
256
TWIEGKEPGC
266
ETIGLLMSSM
276
DDLICHCNGK
286
LGSYKINGRT
296

KAMVACYPGN
306
GTGYVRHCDN
316
PNGDGRCVTC
326
IYYLNKDWDA
336
KVSGGILRIF
346

PEGKAQFADI
356
EPKFDRLLFF
366
WSDRRNPHEV
376
QPAYATRYAI
386
TVWYFDADER
396

AAAKV
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .OGA or .OGA2 or .OGA3 or :3OGA;style chemicals stick;color identity;select .A:252 or .A:254 or .A:299 or .A:303 or .A:310 or .A:313 or .A:315 or .A:327 or .A:329 or .A:343 or .A:366 or .A:374 or .A:375 or .A:376 or .A:383 or .A:385 or .A:387 or .A:389; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ARG252
3.501
ASP254
4.846
MET299
2.637
TYR303
3.343
TYR310
2.817
HIS313
2.408
ASP315
3.407
ILE327
2.858
TYR329
1.700
Residue
Distance (Å)
LEU343
2.260
PHE366
4.491
HIS374
2.378
GLU375
4.967
VAL376
2.123
ARG383
1.802
ALA385
3.872
THR387
4.046
TRP389
3.509
PDB ID: 3HQR      PHD2:Mn:NOG:HIF1-alpha substrate complex
Method X-ray diffraction Resolution 2.00 Å Mutation Yes [2]
PDB Sequence
QTKPLPALKL
193
ALEYIVPCMN
203
KHGICVVDDF
213
LGKETGQQIG
223
DEVRALHDTG
233

KFTDGQLVSQ
243
KSDSSKDIRG
253
DKITWIEGKE
263
PGCETIGLLM
273
SSMDDLIRHC
283

NGKLGSYKIN
293
GRTKAMVACY
303
PGNGTGYVRH
313
VDNPNGDGRC
323
VTCIYYLNKD
333

WDAKVSGGIL
343
RIFPEGKAQF
353
ADIEPKFDRL
363
LFFWSDRRNP
373
HEVQPAYATR
383

YAITVWYFDA
393
DERAAAKVKY
403
LTGEK
Click to Show 3D Structure of This Binding Site
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Residue
Distance (Å)
ARG252
3.726
ASP254
4.363
MET299
3.121
TYR303
4.091
TYR310
2.986
HIS313
3.064
ASP315
3.605
ILE327
3.667
TYR329
2.389
Residue
Distance (Å)
LEU343
3.434
PHE366
4.975
HIS374
2.717
VAL376
3.251
ARG383
2.519
ALA385
3.845
THR387
4.786
TRP389
4.131
PDB ID: 7Q5V      HIF PROLYL HYDROXYLASE 2 (PHD2/EGLN1) IN COMPLEX WITH N-OXALYLGLYCINE (NOG) AND HIF-2 ALPHA CODD (523-542)
Method X-ray diffraction Resolution 1.17 Å Mutation No [3]
PDB Sequence
TKPLPALKLA
194
LEYIVPCMNK
204
HGICVVDDFL
214
GKETGQQIGD
224
EVRALHDTGK
234

FTDGQLVSQK
244
SDSSKDIRGD
254
KITWIEGKEP
264
GCETIGLLMS
274
SMDDLIRHCN
284

GKLGSYKING
294
RTKAMVACYP
304
GNGTGYVRHV
314
DNPNGDGRCV
324
TCIYYLNKDW
334

DAKVSGGILR
344
IFPEGKAQFA
354
DIEPKFDRLL
364
FFWSDRRNPH
374
EVQPAYATRY
384

AITVWYFDAD
394
ERARAKVKYL
404
TGE
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .OGA or .OGA2 or .OGA3 or :3OGA;style chemicals stick;color identity;select .A:252 or .A:254 or .A:299 or .A:303 or .A:310 or .A:313 or .A:315 or .A:327 or .A:329 or .A:343 or .A:358 or .A:366 or .A:374 or .A:375 or .A:376 or .A:383 or .A:385 or .A:387 or .A:389; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ARG252
3.890
ASP254
4.537
MET299
2.553
TYR303
3.350
TYR310
3.062
HIS313
2.616
ASP315
3.278
ILE327
2.719
TYR329
1.829
LEU343
2.277
Residue
Distance (Å)
PRO358
4.908
PHE366
4.076
HIS374
2.680
GLU375
4.885
VAL376
2.181
ARG383
1.958
ALA385
3.623
THR387
3.715
TRP389
3.201
PDB ID: 6YW4      HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with N-oxalylglycine (NOG) and a RaPID-derived silent allosteric cyclic peptide 3C (14-mer)
Method X-ray diffraction Resolution 1.53 Å Mutation No [4]
PDB Sequence
KPLPALKLAL
195
EYIVPAMNKH
205
GICVVDDFLG
215
KETGQQIGDE
225
VRALHDTGKF
235

TDGQDIRGDK
255
ITWIEGKEPG
265
CETIGLLMSS
275
MDDLIRHCNG
285
KLGSYKINGR
295

TKAMVACYPG
305
NGTGYVRHVD
315
NPNGDGRCVT
325
CIYYLNKDWD
335
AKVSGGILRI
345

FPEGKAQFAD
355
IEPKFDRLLF
365
FWSDRRNPHE
375
VQPAYATRYA
385
ITVWYFDADE
395

RAAAKVKYLT
405
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .OGA or .OGA2 or .OGA3 or :3OGA;style chemicals stick;color identity;select .A:252 or .A:254 or .A:299 or .A:303 or .A:310 or .A:313 or .A:315 or .A:327 or .A:329 or .A:343 or .A:358 or .A:366 or .A:374 or .A:376 or .A:383 or .A:385 or .A:387 or .A:389; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ARG252
3.866
ASP254
4.512
MET299
2.559
TYR303
3.178
TYR310
2.998
HIS313
2.455
ASP315
3.293
ILE327
2.593
TYR329
1.889
Residue
Distance (Å)
LEU343
2.356
PRO358
4.767
PHE366
4.296
HIS374
2.605
VAL376
2.476
ARG383
1.875
ALA385
3.633
THR387
4.071
TRP389
3.306
PDB ID: 6YW3      HIF PROLYL HYDROXYLASE 2 (PHD2/ EGLN1) in complex with N-Oxalyl Glycine (NOG), HIF-1ALPHA CODD (556-574) and a RaPID-derived cyclic peptide 3C (14-mer)
Method X-ray diffraction Resolution 2.28 Å Mutation No [4]
PDB Sequence
TKPLPALKLA
194
LEYIVPCMNK
204
HGICVVDDFL
214
GKETGQQIGD
224
EVRALHDTGK
234

FTDGQLVSQK
244
SDSSKDIRGD
254
KITWIEGKEP
264
GCETIGLLMS
274
SMDDLIRHCN
284

GKLGSYKING
294
RTKAMVACYP
304
GNGTGYVRHV
314
DNPNGDGRCV
324
TCIYYLNKDW
334

DAKVSGGILR
344
IFPEGKAQFA
354
DIEPKFDRLL
364
FFWSDRRNPH
374
EVQPAYATRY
384

AITVWYFDAD
394
ERARAKVKYL
404
TGE
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .OGA or .OGA2 or .OGA3 or :3OGA;style chemicals stick;color identity;select .A:252 or .A:254 or .A:299 or .A:301 or .A:303 or .A:310 or .A:313 or .A:315 or .A:327 or .A:329 or .A:343 or .A:358 or .A:366 or .A:374 or .A:376 or .A:383 or .A:385 or .A:387 or .A:389; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ARG252
3.813
ASP254
4.435
MET299
2.348
ALA301
4.905
TYR303
2.528
TYR310
3.277
HIS313
2.586
ASP315
3.323
ILE327
2.216
TYR329
1.983
Residue
Distance (Å)
LEU343
2.617
PRO358
4.972
PHE366
4.485
HIS374
2.675
VAL376
2.823
ARG383
1.815
ALA385
3.429
THR387
4.594
TRP389
3.079
References  Top
REF 1 Structural basis for oxygen degradation domain selectivity of the HIF prolyl hydroxylases. Nat Commun. 2016 Aug 26;7:12673.
REF 2 Structural basis for binding of hypoxia-inducible factor to the oxygen-sensing prolyl hydroxylases. Structure. 2009 Jul 15;17(7):981-9.
REF 3 HIF PROLYL HYDROXYLASE 2 (PHD2/EGLN1) IN COMPLEX WITH N-OXALYLGLYCINE (NOG) AND HIF-2 ALPHA CODD (523-542)
REF 4 Use of cyclic peptides to induce crystallization: case study with prolyl hydroxylase domain 2. Sci Rep. 2020 Dec 15;10(1):21964.

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