Structure of PDB 6plg Chain F Binding Site BS01

Receptor Information
>6plg Chain F (length=299) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VLISDSLDPCCRKILQDGGLQVVEKQNLSKEELIAELQDCEGLIVRSATK
VTADVINAAEKLQVVGRAGTGVDNVDLEAATRKGILVMNTPNGNSLSAAE
LTCGMIMCLARQIPQATASMKDGKWERKKFMGTELNGKTLGILGLGRIGR
EVATRMQSFGMKTIGYDPIISPEVSASFGVQQLPLEEIWPLCDFITVHTP
LLPSTTGLLNDNTFAQCKKGVRVVNCARGGIVDEGALLRALQSGQCAGAA
LDVFTEEPPRDRALVDHENVISCPHLGASTKEAQSRCGEEIAVQFVDMV
Ligand information
Ligand IDONS
InChIInChI=1S/C26H21Cl2N3O4/c1-31-20-9-8-19(27)23(28)18(20)11-21(31)24(32)30-26(13-35-14-26)17-6-4-15(5-7-17)22(25(33)34)16-3-2-10-29-12-16/h2-12,22H,13-14H2,1H3,(H,30,32)(H,33,34)/t22-/m0/s1
InChIKeyLHTXTAIWLHZCIX-QFIPXVFZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7Cn1c2ccc(c(c2cc1C(=O)NC3(COC3)c4ccc(cc4)[C@@H](c5cccnc5)C(=O)O)Cl)Cl
CACTVS 3.385Cn1c(cc2c(Cl)c(Cl)ccc12)C(=O)NC3(COC3)c4ccc(cc4)[C@H](C(O)=O)c5cccnc5
CACTVS 3.385Cn1c(cc2c(Cl)c(Cl)ccc12)C(=O)NC3(COC3)c4ccc(cc4)[CH](C(O)=O)c5cccnc5
ACDLabs 12.01OC(=O)C(c1cccnc1)c2ccc(cc2)C5(NC(c3cc4c(n3C)ccc(c4Cl)Cl)=O)COC5
OpenEye OEToolkits 2.0.7Cn1c2ccc(c(c2cc1C(=O)NC3(COC3)c4ccc(cc4)C(c5cccnc5)C(=O)O)Cl)Cl
FormulaC26 H21 Cl2 N3 O4
Name(2S)-(4-{3-[(4,5-dichloro-1-methyl-1H-indole-2-carbonyl)amino]oxetan-3-yl}phenyl)(pyridin-3-yl)acetic acid
ChEMBL
DrugBank
ZINC
PDB chain6plg Chain F 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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PDB6plg Inhibition of 3-phosphoglycerate dehydrogenase (PHGDH) by indole amides abrogates de novo serine synthesis in cancer cells.
Resolution2.93 Å
Binding residue
(original residue number in PDB)		G154 R155 I156 D175 P176 I177 H206 T207 P208 L216 R236
Binding residue
(residue number reindexed from 1)		G146 R147 I148 D167 P168 I169 H198 T199 P200 L208 R228
Annotation score1
Binding affinityBindingDB: IC50=15nM
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:6plg, PDBe:6plg, PDBj:6plg
PDBsum6plg
PubMed31327531
UniProtO43175|SERA_HUMAN D-3-phosphoglycerate dehydrogenase (Gene Name=PHGDH)

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