Binding Site Information of Target
| 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 | |||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| Ligand Name: NADH | Ligand Info | |||||
| Structure Description | CRYSTAL STRUCTURE PHGDH IN COMPLEX WITH NADH AND 3-PHOSPHOGLYCERATE AT 1.77 A RESOLUTION | PDB:6CWA | ||||
| Method | X-ray diffraction | Resolution | 1.77 Å | Mutation | No | [1] |
| PDB Sequence |
RKVLISDSLD
15 PCCRKILQDG25 GLQVVEKQNL35 SKEELIAELQ45 DCEGLIVRSA55 TKVTADVINA 65 AEKLQVVGRA75 GTGVDNVDLE85 AATRKGILVM95 NTPNGNSLSA105 AELTCGMIMC 115 LARQIPQATA125 SMKDGKWERK135 KFMGTELNGK145 TLGILGLGRI155 GREVATRMQS 165 FGMKTIGYDP175 IISPEVSASF185 GVQQLPLEEI195 WPLCDFITVH205 TPLLPSTTGL 215 LNDNTFAQCK225 KGVRVVNCAR235 GGIVDEGALL245 RALQSGQCAG255 AALDVFTEEP 265 PRDRALVDHE275 NVISCPHLGA285 STKEAQSRCG295 EEIAVQFVD
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THR77
2.842
GLY78
4.805
PRO98
4.257
ASN101
3.186
SER102
4.181
ALA105
3.687
LEU150
4.240
GLY151
3.600
LEU152
4.347
GLY153
3.310
ARG154
3.009
ILE155
2.996
GLY156
4.470
TYR173
3.408
ASP174
2.660
PRO175
3.294
ILE176
3.156
ILE177
4.504
|
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| Ligand Name: Nicotinamide-Adenine-Dinucleotide | Ligand Info | |||||
| Structure Description | Crystal structure of human 3-phosphoglycerate dehydrogenase | PDB:2G76 | ||||
| Method | X-ray diffraction | Resolution | 1.70 Å | Mutation | No | [2] |
| 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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|
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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
|
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: 3-Phosphoglyceric Acid | Ligand Info | |||||
| Structure Description | CRYSTAL STRUCTURE PHGDH IN COMPLEX WITH NADH AND 3-PHOSPHOGLYCERATE AT 1.77 A RESOLUTION | PDB:6CWA | ||||
| Method | X-ray diffraction | Resolution | 1.77 Å | Mutation | No | [1] |
| PDB Sequence |
RKVLISDSLD
15 PCCRKILQDG25 GLQVVEKQNL35 SKEELIAELQ45 DCEGLIVRSA55 TKVTADVINA 65 AEKLQVVGRA75 GTGVDNVDLE85 AATRKGILVM95 NTPNGNSLSA105 AELTCGMIMC 115 LARQIPQATA125 SMKDGKWERK135 KFMGTELNGK145 TLGILGLGRI155 GREVATRMQS 165 FGMKTIGYDP175 IISPEVSASF185 GVQQLPLEEI195 WPLCDFITVH205 TPLLPSTTGL 215 LNDNTFAQCK225 KGVRVVNCAR235 GGIVDEGALL245 RALQSGQCAG255 AALDVFTEEP 265 PRDRALVDHE275 NVISCPHLGA285 STKEAQSRCG295 EEIAVQFVD
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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 .3PG or .3PG2 or .3PG3 or :33PG;style chemicals stick;color identity;select .A:53 or .A:54 or .A:74 or .A:75 or .A:76 or .A:77 or .A:78 or .A:80 or .A:101 or .A:234 or .A:235 or .A:282 or .A:285 or .A:286 or .A:291; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: D-malate | Ligand Info | |||||
| Structure Description | Crystal structure of human 3-phosphoglycerate dehydrogenase | PDB:2G76 | ||||
| Method | X-ray diffraction | Resolution | 1.70 Å | Mutation | No | [2] |
| 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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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .MLT or .MLT2 or .MLT3 or :3MLT;style chemicals stick;color identity;select .A:53 or .A:54 or .A:74 or .A:75 or .A:76 or .A:77 or .A:101 or .A:235 or .A:282 or .A:284 or .A:285 or .A:291; 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-[(1~{R})-1-[(2-methyl-5-phenyl-pyrazol-3-yl)carbonylamino]ethyl]benzoic acid | Ligand Info | |||||
| Structure Description | Crystal structure of PHGDH in complex with compound 15 | PDB:6RJ3 | ||||
| Method | X-ray diffraction | Resolution | 1.42 Å | Mutation | No | [1] |
| PDB Sequence |
RKVLISDSLD
15 PCCRKILQDG25 GLQVVEKQNL35 SKEELIAELQ45 DCEGLIVRSA55 TKVTADVINA 65 AEKLQVVGRA75 GTGVDNVDLE85 AATRKGILVM95 NTPNGNSLSA105 AELTCGMIMC 115 LARQIPQATA125 SMKDGKWERK135 KFMGTELNGK145 TLGILGLGRI155 GREVATRMQS 165 FGMKTIGYDP175 IISPEVSASF185 GVQQLPLEEI195 WPLCDFITVH205 TPLLPSTTGL 215 LNDNTFAQCK225 KGVRVVNCAR235 GGIVDEGALL245 RALQSGQCAG255 AALDVFTEEP 265 PRDRALVDHE275 NVISCPHLGA285 STKEAQSRCG295 EEIAVQF
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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 .K58 or .K582 or .K583 or :3K58;style chemicals stick;color identity;select .A:98 or .A:150 or .A:151 or .A:152 or .A:153 or .A:155 or .A:173 or .A:174 or .A:175 or .A:176 or .A:177 or .A:192 or .A:205 or .A:206 or .A:207 or .A:209 or .A:211 or .A:212 or .A:215; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: (1beta,6beta,7beta,8alpha,9beta,10alpha,13alpha,14r,16beta)-1,6,7,14-Tetrahydroxy-7,20-Epoxykauran-15-One | Ligand Info | |||||
| Structure Description | PHGDH covalently linked to oridonin | PDB:7DKM | ||||
| 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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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .ODN or .ODN2 or .ODN3 or :3ODN;style chemicals stick;color identity;select .A:18 or .A:21 or .A:22 or .A:25 or .A:297; 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-{(1S)-1-[(5-chloro-6-{[(5S)-2-oxo-1,3-oxazolidin-5-yl]methoxy}-1H-indole-2-carbonyl)amino]-2-hydroxyethyl}benzoic acid | Ligand Info | |||||
| Structure Description | Crystal structure of human PHGDH complexed with Compound 1 | PDB:6PLF | ||||
| Method | X-ray diffraction | Resolution | 1.70 Å | Mutation | No | [4] |
| 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 DMVKG |
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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 .ONV or .ONV2 or .ONV3 or :3ONV;style chemicals stick;color identity;select .A:151 or .A:152 or .A:153 or .A:154 or .A:155 or .A:156 or .A:174 or .A:175 or .A:176 or .A:177 or .A:178 or .A:193 or .A:206 or .A:207 or .A:208 or .A:210 or .A:212 or .A:213 or .A:216; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 2-methyl-~{N}-[(1~{R})-1-[4-(methylsulfonylcarbamoyl)phenyl]ethyl]-5-phenyl-pyrazole-3-carboxamide | Ligand Info | |||||
| Structure Description | Crystal structure of PHGDH in complex with compound 39 | PDB:6RJ5 | ||||
| Method | X-ray diffraction | Resolution | 1.89 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 M |
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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 .K5N or .K5N2 or .K5N3 or :3K5N;style chemicals stick;color identity;select .A:77 or .A:96 or .A:98 or .A:150 or .A:151 or .A:152 or .A:153 or .A:155 or .A:173 or .A:174 or .A:175 or .A:176 or .A:177 or .A:192 or .A:205 or .A:206 or .A:207 or .A:209 or .A:211 or .A:212 or .A:215; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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THR77
3.664
ASN96
4.872
PRO98
3.429
LEU150
3.641
GLY151
3.615
LEU152
4.437
GLY153
3.777
ILE155
4.020
TYR173
3.201
ASP174
2.859
PRO175
3.356
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| Ligand Name: 2-[4-[(1~{S})-1-[[4,5-bis(chloranyl)-1,6-dimethyl-indol-2-yl]carbonylamino]-2-oxidanyl-ethyl]phenyl]sulfonylethanoic acid | Ligand Info | |||||
| Structure Description | Crystal structure of PHGDH in complex with BI-4924 | PDB:6RJ6 | ||||
| Method | X-ray diffraction | Resolution | 1.98 Å | Mutation | No | [1] |
| PDB Sequence |
NGSLSAAELT
109 CGMIMCLARQ119 IPQATASMKD129 GKWERKKFMG139 TELNGKTLGI149 LGLGRIGREV 159 ATRMQSFGMK169 TIGYDPIISP179 EVSASFGVQQ189 LPLEEIWPLC199 DFITVHTPLL 209 PSTTGLLNDN219 TFAQCKKGVR229 VVNCARGGIV239 DEGALLRALQ249 SGQCAGAALD 259 VFTEEPPRDR269 ALVDHENVIS279 CPHLGASTKE289 AQSRCGEEIA299 VQFV |
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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 .K5K or .K5K2 or .K5K3 or :3K5K;style chemicals stick;color identity;select .A:150 or .A:151 or .A:152 or .A:153 or .A:154 or .A:155 or .A:156 or .A:173 or .A:174 or .A:175 or .A:176 or .A:177 or .A:192 or .A:205 or .A:206 or .A:207 or .A:209 or .A:211 or .A:212 or .A:215; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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LEU150
3.779
GLY151
3.313
LEU152
4.340
GLY153
3.831
ARG154
3.116
ILE155
3.163
GLY156
4.453
TYR173
3.416
ASP174
2.977
PRO175
3.360
|
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| Ligand Name: N-[(1R)-1-[4-(acetylsulfamoyl)phenyl]ethyl]-2-methyl-5-phenylpyrazole-3-carboxamide | Ligand Info | |||||
| Structure Description | Crystal structure of PHGDH in complex with compound 40 | PDB:6RJ2 | ||||
| Method | X-ray diffraction | Resolution | 2.00 Å | Mutation | No | [1] |
| PDB Sequence |
VLISDSLDPC
17 CRKILQDGGL27 QVVEKQNLSK37 EELIAELQDC47 EGLIVRSATK57 VTADVINAAE 67 KLQVVGRAGT77 GVDNVDLEAA87 TRKGILVMNT97 PNGNSLSAAE107 LTCGMIMCLA 117 RQIPQATASM127 KDGKWERKKF137 MGTELNGKTL147 GILGLGRIGR157 EVATRMQSFG 167 MKTIGYDPII177 SPEVSASFGV187 QQLPLEEIWP197 LCDFITVHTP207 LLPSTTGLLN 217 DNTFAQCKKG227 VRVVNCARGG237 IVDEGALLRA247 LQSGQCAGAA257 LDVFTEEPPR 267 DRALVDHENV277 ISCPHLGAST287 KEAQSRCGEE297 IAVQFVDMV
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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 .K52 or .K522 or .K523 or :3K52;style chemicals stick;color identity;select .A:98 or .A:99 or .A:102 or .A:150 or .A:151 or .A:152 or .A:153 or .A:154 or .A:155 or .A:156 or .A:173 or .A:174 or .A:175 or .A:176 or .A:177 or .A:192 or .A:205 or .A:206 or .A:207 or .A:209 or .A:211 or .A:212 or .A:215 or .A:235; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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PRO98
4.001
ASN99
3.784
SER102
3.204
LEU150
4.093
GLY151
3.845
LEU152
4.201
GLY153
3.668
ARG154
3.279
ILE155
3.083
GLY156
4.630
TYR173
3.452
ASP174
2.799
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| Ligand Name: N-cyclopropyl-1-methyl-3-phenyl-1H-pyrazole-5-carboxamide | Ligand Info | |||||
| Structure Description | Crystal structure of PHGDH in complex with compound 9 | PDB:6RIH | ||||
| Method | X-ray diffraction | Resolution | 2.15 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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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .K4T or .K4T2 or .K4T3 or :3K4T;style chemicals stick;color identity;select .A:150 or .A:151 or .A:152 or .A:153 or .A:173 or .A:174 or .A:175 or .A:176 or .A:177 or .A:192 or .A:205 or .A:206 or .A:207 or .A:209 or .A:211 or .A:212 or .A:215; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: (2S)-(4-{3-[(4,5-dichloro-1-methyl-1H-indole-2-carbonyl)amino]oxetan-3-yl}phenyl)(pyridin-3-yl)acetic acid | Ligand Info | |||||
| Structure Description | Crystal structure of human PHGDH complexed with Compound 15 | PDB:6PLG | ||||
| Method | X-ray diffraction | Resolution | 2.93 Å | Mutation | No | [4] |
| PDB Sequence |
LRKVLISDSL
15 DPCCRKILQD25 GGLQVVEKQN35 LSKEELIAEL45 QDCEGLIVRS55 ATKVTADVIN 65 AAEKLQVVGR75 AGTGVDNVDL85 EAATRKGILV95 MNTPNGNSLS105 AAELTCGMIM 115 CLARQIPQAT125 ASMKDGKWER135 KKFMGTELNG145 KTLGILGLGR155 IGREVATRMQ 165 SFGMKTIGYD175 PIISPEVSAS185 FGVQQLPLEE195 IWPLCDFITV205 HTPLLPSTTG 215 LLNDNTFAQC225 KKGVRVVNCA235 RGGIVDEGAL245 LRALQSGQCA255 GAALDVFTEE 265 PPRDRALVDH275 ENVISCPHLG285 ASTKEAQSRC295 GEEIAVQFVD305 MVK |
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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 .ONS or .ONS2 or .ONS3 or :3ONS;style chemicals stick;color identity;select .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:210 or .A:212 or .A:213 or .A:216 or .A:235 or .A:236; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
LEU151
4.573
GLY152
4.248
LEU153
3.768
GLY154
3.497
ARG155
3.171
ILE156
3.534
GLY157
4.567
TYR174
3.627
ASP175
2.586
PRO176
3.389
ILE177
3.519
|
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| Ligand Name: 1-methyl-1H-indol-5-amine | Ligand Info | |||||
| Structure Description | Crystal structure of human 3-phosphoglycerate dehydrogenase in complex with 5-amino-1-methyl-1H-indole | PDB:5OFM | ||||
| Method | X-ray diffraction | Resolution | 1.50 Å | Mutation | No | [5] |
| PDB Sequence |
NGNSLSAAEL
109 TCGMIMCLAR119 QIPQATASMK129 DGKWERKKFM139 GTELNGKTLG149 ILGLGRIGRE 159 VATRMQSFGM169 KTIGYDPIIS179 PEVSASFGVQ189 QLPLEEIWPL199 CDFITVHTPL 209 LPSTTGLLND219 NTFAQCKKGV229 RVVNCARGGI239 VDEGALLRAL249 QSGQCAGAAL 259 DVFTEEPPRD269 RALVDHENVI279 SCPHLGASTK289 EAQSR
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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 .9TT or .9TT2 or .9TT3 or :39TT;style chemicals stick;color identity;select .B:151 or .B:152 or .B:174 or .B:175 or .B:176 or .B:207 or .B:208 or .B:210 or .B:212 or .B:213 or .B:216; 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-(1,3-Oxazol-5-yl)aniline | Ligand Info | |||||
| Structure Description | Crystal structure of human 3-phosphoglycerate dehydrogenase in complex with 3-(1,3-oxazol-5-yl)aniline. | PDB:5NZQ | ||||
| Method | X-ray diffraction | Resolution | 1.50 Å | Mutation | No | [6] |
| PDB Sequence |
NGNSLSAAEL
109 TCGMIMCLAR119 QIPQATASMK129 DGKWERKKFM139 GTELNGKTLG149 ILGLGRIGRE 159 VATRMQSFGM169 KTIGYDPIIS179 PEVSASFGVQ189 QLPLEEIWPL199 CDFITVHTPL 209 LPSTTGLLND219 NTFAQCKKGV229 RVVNCARGGI239 VDEGALLRAL249 QSGQCAGAAL 259 DVFTEEPPRD269 RALVDHENVI279 SCPHLGASTK289 EAQSR
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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 .5AO or .5AO2 or .5AO3 or :35AO;style chemicals stick;color identity;select .B:151 or .B:152 or .B:174 or .B:175 or .B:176 or .B:193 or .B:207 or .B:208 or .B:210 or .B:212 or .B:213 or .B:216; 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-Chloro-4-fluorobenzamide | Ligand Info | |||||
| Structure Description | Crystal structure of human 3-phosphoglycerate dehydrogenase in complex with 3-Chloro-4-fluorobenzamide | PDB:5OFW | ||||
| Method | X-ray diffraction | Resolution | 1.50 Å | Mutation | No | [6] |
| PDB Sequence |
NGNSLSAAEL
109 TCGMIMCLAR119 QIPQATASMK129 DGKWERKKFM139 GTELNGKTLG149 ILGLGRIGRE 159 VATRMQSFGM169 KTIGYDPIIS179 PEVSASFGVQ189 QLPLEEIWPL199 CDFITVHTPL 209 LPSTTGLLND219 NTFAQCKKGV229 RVVNCARGGI239 VDEGALLRAL249 QSGQCAGAAL 259 DVFTEEPPRD269 RALVDHENVI279 SCPHLGASTK289 EAQSR
|
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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 .9TW or .9TW2 or .9TW3 or :39TW;style chemicals stick;color identity;select .B:151 or .B:152 or .B:174 or .B:175 or .B:176 or .B:193 or .B:207 or .B:208 or .B:210 or .B:212 or .B:213 or .B:216; 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-Fluoro-2-methylbenzoic acid | Ligand Info | |||||
| Structure Description | Crystal structure of human 3-phosphoglycerate dehydrogenase in complex with 5-fluoro-2-methylbenzoic acid | PDB:5OFV | ||||
| Method | X-ray diffraction | Resolution | 1.50 Å | Mutation | No | [6] |
| PDB Sequence |
NGNSLSAAEL
109 TCGMIMCLAR119 QIPQATASMK129 DGKWERKKFM139 GTELNGKTLG149 ILGLGRIGRE 159 VATRMQSFGM169 KTIGYDPIIS179 PEVSASFGVQ189 QLPLEEIWPL199 CDFITVHTPL 209 LPSTTGLLND219 NTFAQCKKGV229 RVVNCARGGI239 VDEGALLRAL249 QSGQCAGAAL 259 DVFTEEPPRD269 RALVDHENVI279 SCPHLGASTK289 EAQSR
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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 .9TZ or .9TZ2 or .9TZ3 or :39TZ;style chemicals stick;color identity;select .B:151 or .B:152 or .B:153 or .B:174 or .B:175 or .B:176 or .B:193 or .B:206 or .B:207 or .B:208 or .B:210 or .B:212 or .B:213 or .B:216; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: Benzo[d]isoxazol-3-ol | Ligand Info | |||||
| Structure Description | Crystal structure of human 3-phosphoglycerate dehydrogenase in complex with 3-Hydroxybenzisoxazole | PDB:5NZP | ||||
| Method | X-ray diffraction | Resolution | 1.30 Å | Mutation | No | [6] |
| PDB Sequence |
NGNSLSAAEL
109 TCGMIMCLAR119 QIPQATASMK129 DGKWERKKFM139 GTELNGKTLG149 ILGLGRIGRE 159 VATRMQSFGM169 KTIGYDPIIS179 PEVSASFGVQ189 QLPLEEIWPL199 CDFITVHTPL 209 LPSTTGLLND219 NTFAQCKKGV229 RVVNCARGGI239 VDEGALLRAL249 QSGQCAGAAL 259 DVFTEEPPRD269 RALVDHENVI279 SCPHLGASTK289 EAQSR
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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 .9EW or .9EW2 or .9EW3 or :39EW;style chemicals stick;color identity;select .B:151 or .B:152 or .B:174 or .B:175 or .B:176 or .B:193 or .B:207 or .B:208 or .B:210 or .B:212 or .B:213 or .B:216; 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-Methyl-3-phenyl-1H-pyrazol-5-amine | Ligand Info | |||||
| Structure Description | Crystal structure of human 3-phosphoglycerate dehydrogenase in complex with 1-methyl-3-phenyl-1H-pyrazol-5-amine | PDB:5NZO | ||||
| Method | X-ray diffraction | Resolution | 1.29 Å | Mutation | No | [6] |
| PDB Sequence |
NGNSLSAAEL
109 TCGMIMCLAR119 QIPQATASMK129 DGKWERKKFM139 GTELNGKTLG149 ILGLGRIGRE 159 VATRMQSFGM169 KTIGYDPIIS179 PEVSASFGVQ189 QLPLEEIWPL199 CDFITVHTPL 209 LPSTTGLLND219 NTFAQCKKGV229 RVVNCARGGI239 VDEGALLRAL249 QSGQCAGAAL 259 DVFTEEPPRD269 RALVDHENVI279 SCPHLGASTK289 EAQSR
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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 .9EZ or .9EZ2 or .9EZ3 or :39EZ;style chemicals stick;color identity;select .B:151 or .B:152 or .B:174 or .B:175 or .B:176 or .B:177 or .B:193 or .B:207 or .B:208 or .B:210 or .B:212 or .B:213 or .B:216; 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-(3-Chloro-4-methoxyphenyl)acetamide | Ligand Info | |||||
| Structure Description | Crystal structure of human 3-phosphoglycerate dehydrogenase in complex with N-(3-chloro-4-methoxyphenyl) acetamide | PDB:5N53 | ||||
| Method | X-ray diffraction | Resolution | 1.48 Å | Mutation | No | [6] |
| PDB Sequence |
NGNSLSAAEL
109 TCGMIMCLAR119 QIPQATASMK129 DGKWERKKFM139 GTELNGKTLG149 ILGLGRIGRE 159 VATRMQSFGM169 KTIGYDPIIS179 PEVSASFGVQ189 QLPLEEIWPL199 CDFITVHTPL 209 LPSTTGLLND219 NTFAQCKKGV229 RVVNCARGGI239 VDEGALLRAL249 QSGQCAGAAL 259 DVFTEEPPRD269 RALVDHENVI279 SCPHLGASTK289 EAQSR
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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 .8NB or .8NB2 or .8NB3 or :38NB;style chemicals stick;color identity;select .B:151 or .B:152 or .B:174 or .B:175 or .B:176 or .B:177 or .B:207 or .B:208 or .B:210 or .B:212 or .B:213 or .B:216; 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 | Intracellular Trapping of the Selective Phosphoglycerate Dehydrogenase (PHGDH) Inhibitor BI-4924 Disrupts Serine Biosynthesis. J Med Chem. 2019 Sep 12;62(17):7976-7997. | ||||
| REF 2 | Crystal structure of human 3-phosphoglycerate dehydrogenase | ||||
| 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 | Inhibition of 3-phosphoglycerate dehydrogenase (PHGDH) by indole amides abrogates de novo serine synthesis in cancer cells. Bioorg Med Chem Lett. 2019 Sep 1;29(17):2503-2510. | ||||
| REF 5 | Crystal structure of human 3-phosphoglycerate dehydrogenase in complex with 5-amino-1-methyl-1H-indole | ||||
| REF 6 | Validating and enabling phosphoglycerate dehydrogenase (PHGDH) as a target for fragment-based drug discovery in PHGDH-amplified breast cancer. Oncotarget. 2016 Aug 22;9(17):13139-13153. | ||||
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