Target Binding Site Detail
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T15139 | Target Info | |||
| Target Name | Phosphoglycerate dehydrogenase (PHGDH) | ||||
| Synonyms | PGDH3; Malate dehydrogenase; D-3-phosphoglycerate dehydrogenase; 3-PGDH; 2-oxoglutarate reductase | ||||
| Target Type | Literature-reported Target | ||||
| Gene Name | PHGDH | ||||
| Biochemical Class | Short-chain dehydrogenases reductase | ||||
| UniProt ID | |||||
| Ligand General Information | Top | ||||
|---|---|---|---|---|---|
| Ligand Name | Nicotinamide-Adenine-Dinucleotide | Ligand Info | |||
| Canonical SMILES | C1=CC(=C[N+](=C1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)N4C=NC5=C(N=CN=C54)N)O)O)O)O)C(=O)N | ||||
| InChI | 1S/C21H27N7O14P2/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(32)14(30)11(41-21)6-39-44(36,37)42-43(34,35)38-5-10-13(29)15(31)20(40-10)27-3-1-2-9(4-27)18(23)33/h1-4,7-8,10-11,13-16,20-21,29-32H,5-6H2,(H5-,22,23,24,25,33,34,35,36,37)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1 | ||||
| InChIKey | BAWFJGJZGIEFAR-NNYOXOHSSA-N | ||||
| PubChem Compound ID | 5892 | ||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| PDB ID: 2G76 Crystal structure of human 3-phosphoglycerate dehydrogenase | ||||||
| Method | X-ray diffraction | Resolution | 1.70 Å | Mutation | No | [1] |
| PDB Sequence |
LRKVLISDSL
14 DPCCRKILQD24 GGLQVVEKQN34 LSKEELIAEL44 QDCEGLIVRS54 ATKVTADVIN 64 AAEKLQVVGR74 AGTGVDNVDL84 EAATRKGILV94 MNTPNGNSLS104 AAELTCGMIM 114 CLARQIPQAT124 ASMKDGKWER134 KKFMGTELNG144 KTLGILGLGR154 IGREVATRMQ 164 SFGMKTIGYD174 PIISPEVSAS184 FGVQQLPLEE194 IWPLCDFITV204 HTPLLPSTTG 214 LLNDNTFAQC224 KKGVRVVNCA234 RGGIVDEGAL244 LRALQSGQCA254 GAALDVFTEE 264 PPRDRALVDH274 ENVISCPHLG284 ASTKEAQSRC294 GEEIAVQFVD304 MV |
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|
|
THR77
2.771
GLY78
4.618
PRO98
4.208
ASN101
3.732
SER102
4.445
ALA105
3.722
LEU150
4.162
GLY151
3.496
LEU152
4.325
GLY153
3.420
ARG154
2.906
ILE155
2.913
GLY156
4.414
TYR173
3.294
ASP174
2.661
PRO175
3.307
ILE176
3.924
ILE177
4.229
|
|||||
| PDB ID: 7CVP The Crystal Structure of human PHGDH from Biortus. | ||||||
| Method | X-ray diffraction | Resolution | 2.50 Å | Mutation | No | [2] |
| PDB Sequence |
RKVLISDPCC
19 RKILQDGELQ46 DCEGLIVRSV59 TADVIVVGRA76 GTLVMNTPNG101 NSLSAAELTC 111 GMIMCLARQI121 PQATASMKDG131 KWERKKFMGT141 ELNGKTLGIL151 GLGRIGREVA 161 TRMQSFGMKT171 IGYDPIISPE181 VSASFGVQQL191 PLEEIWPLCD201 FITVHTPLLP 211 STTGLLNDNT221 FAQCKKGVRV231 VNCARGGIVD241 EGALLRALQS251 GQCAGAALDV 261 FTEEPPRDRA271 LVDHENVISC281 PHLGASTKEA291 QSRCGEEIAV301 QFVD |
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|
|
THR78
3.668
PRO99
4.253
ASN102
3.824
SER103
4.448
ALA106
4.232
LEU151
4.349
GLY152
3.162
LEU153
3.918
GLY154
3.095
ARG155
2.948
ILE156
2.936
GLY157
4.459
TYR174
3.335
ASP175
2.404
PRO176
3.178
ILE177
3.221
ILE178
3.186
HIS206
3.629
|
|||||
| PDB ID: 7DKM PHGDH covalently linked to oridonin | ||||||
| Method | X-ray diffraction | Resolution | 1.70 Å | Mutation | No | [3] |
| PDB Sequence |
NLRKVLISDS
14 LDPCCRKILQ24 DGGLQVVEKQ34 NLSKEELIAE44 LQDCEGLIVR54 SATKVTADVI 64 NAAEKLQVVG74 RAGTGVDNVD84 LEAATRKGIL94 VMNTPNGNSL104 SAAELTCGMI 114 MCLARQIPQA124 TASMKDGKWE134 RKKFMGTELN144 GKTLGILGLG154 RIGREVATRM 164 QSFGMKTIGY174 DPIISPEVSA184 SFGVQQLPLE194 EIWPLCDFIT204 VHTPLLPSTT 214 GLLNDNTFAQ224 CKKGVRVVNC234 ARGGIVDEGA244 LLRALQSGQC254 AGAALDVFTE 264 EPPRDRALVD274 HENVISCPHL284 GASTKEAQSR294 CGEEIAVQFV304 DMVKLE |
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|
|
THR78
3.473
GLY79
4.759
PRO99
3.938
ASN102
3.817
SER103
4.636
ALA106
3.849
LEU151
4.153
GLY152
3.435
LEU153
4.291
GLY154
3.369
ARG155
2.835
ILE156
2.919
GLY157
4.383
TYR174
3.480
ASP175
2.613
PRO176
3.359
ILE177
3.173
ILE178
4.219
|
|||||
| PDB ID: 5N6C Crystal structure of human 3-phosphoglycerate dehydrogenase in complex with NAD and L-Tartrate | ||||||
| Method | X-ray diffraction | Resolution | 2.30 Å | Mutation | No | [4] |
| PDB Sequence |
AKVLISDSLD
16 PCCRKILQDG26 GLQVVEKQNL36 SKEELIAELQ46 DCEGLIVRSA56 TKVTADVINA 66 AEKLQVVGRA76 GTGVDNVDLE86 AATRKGILVM96 NTPNGNSLSA106 AELTCGMIMC 116 LARQIPQATA126 SMKDGKWERK136 KFMGTELNGK146 TLGILGLGRI156 GREVATRMQS 166 FGMKTIGYDP176 IISPEVSASF186 GVQQLPLEEI196 WPLCDFITVH206 TPLLPSTTGL 216 LNDNTFAQCK226 KGVRVVNCAR236 GGIVDEGALL246 RALQSGQCAG256 AALDVFTEEP 266 PRDRALVDHE276 NVISCPHLGA286 STKEAQSRCG296 EEIAVQFVDM306 |
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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 .NAD or .NAD2 or .NAD3 or :3NAD;style chemicals stick;color identity;select .A:78 or .A:79 or .A:99 or .A:102 or .A:103 or .A:106 or .A:151 or .A:152 or .A:153 or .A:154 or .A:155 or .A:156 or .A:157 or .A:174 or .A:175 or .A:176 or .A:177 or .A:178 or .A:206 or .A:207 or .A:208 or .A:209 or .A:210 or .A:212 or .A:213 or .A:216 or .A:234 or .A:235 or .A:236 or .A:239 or .A:260 or .A:261 or .A:283 or .A:284 or .A:285 or .A:286; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
THR78
3.076
GLY79
4.936
PRO99
4.255
ASN102
4.102
SER103
4.543
ALA106
3.925
LEU151
4.068
GLY152
3.421
LEU153
4.233
GLY154
3.626
ARG155
2.845
ILE156
3.033
GLY157
4.422
TYR174
3.493
ASP175
2.717
PRO176
3.398
ILE177
3.329
ILE178
4.476
|
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| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | Crystal structure of human 3-phosphoglycerate dehydrogenase | ||||
| REF 2 | The Crystal Structure of human PHGDH from Biortus. | ||||
| REF 3 | Biophysical and biochemical properties of PHGDH revealed by studies on PHGDH inhibitors. Cell Mol Life Sci. 2021 Dec 31;79(1):27. | ||||
| REF 4 | Structural insights into the enzymatic activity and potential substrate promiscuity of human 3-phosphoglycerate dehydrogenase (PHGDH). Oncotarget. 2017 Nov 6;8(61):104478-104491. | ||||
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