Structure of PDB 6rj6 Chain A Binding Site BS01

Receptor Information
>6rj6 Chain A (length=204) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NGSLSAAELTCGMIMCLARQIPQATASMKDGKWERKKFMGTELNGKTLGI
LGLGRIGREVATRMQSFGMKTIGYDPIISPEVSASFGVQQLPLEEIWPLC
DFITVHTPLLPSTTGLLNDNTFAQCKKGVRVVNCARGGIVDEGALLRALQ
SGQCAGAALDVFTEEPPRDRALVDHENVISCPHLGASTKEAQSRCGEEIA
VQFV
Ligand information
Ligand IDK5K
InChIInChI=1S/C21H20Cl2N2O6S/c1-11-7-16-14(20(23)19(11)22)8-17(25(16)2)21(29)24-15(9-26)12-3-5-13(6-4-12)32(30,31)10-18(27)28/h3-8,15,26H,9-10H2,1-2H3,(H,24,29)(H,27,28)/t15-/m1/s1
InChIKeyCJEJFFCPVBZSIE-OAHLLOKOSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Cn1c(cc2c(Cl)c(Cl)c(C)cc12)C(=O)N[CH](CO)c3ccc(cc3)[S](=O)(=O)CC(O)=O
OpenEye OEToolkits 2.0.7Cc1cc2c(cc(n2C)C(=O)N[C@H](CO)c3ccc(cc3)S(=O)(=O)CC(=O)O)c(c1Cl)Cl
OpenEye OEToolkits 2.0.7Cc1cc2c(cc(n2C)C(=O)NC(CO)c3ccc(cc3)S(=O)(=O)CC(=O)O)c(c1Cl)Cl
CACTVS 3.385Cn1c(cc2c(Cl)c(Cl)c(C)cc12)C(=O)N[C@H](CO)c3ccc(cc3)[S](=O)(=O)CC(O)=O
FormulaC21 H20 Cl2 N2 O6 S
Name2-[4-[(1~{S})-1-[[4,5-bis(chloranyl)-1,6-dimethyl-indol-2-yl]carbonylamino]-2-oxidanyl-ethyl]phenyl]sulfonylethanoic acid
ChEMBLCHEMBL4520837
DrugBank
ZINC
PDB chain6rj6 Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6rj6 Intracellular Trapping of the Selective Phosphoglycerate Dehydrogenase (PHGDH) InhibitorBI-4924Disrupts Serine Biosynthesis.
Resolution1.984 Å
Binding residue
(original residue number in PDB)		G151 R154 I155 Y173 D174 P175 I176 I177 H205 T206 P207 T212
Binding residue
(residue number reindexed from 1)		G52 R55 I56 Y74 D75 P76 I77 I78 H106 T107 P108 T113
Annotation score1
Binding affinityMOAD: ic50=2nM
PDBbind-CN: -logKd/Ki=8.52,IC50=3nM
BindingDB: IC50=3.0nM
Enzymatic activity
Enzyme Commision number 1.1.1.37: malate dehydrogenase.
1.1.1.399: 2-oxoglutarate reductase.
1.1.1.95: phosphoglycerate dehydrogenase.
Gene Ontology
Molecular Function
GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
GO:0051287 NAD binding

View graph for
Molecular Function
External links
PDB RCSB:6rj6, PDBe:6rj6, PDBj:6rj6
PDBsum6rj6
PubMed31365252
UniProtO43175|SERA_HUMAN D-3-phosphoglycerate dehydrogenase (Gene Name=PHGDH)

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