Structure of PDB 6plf Chain A Binding Site BS01

Receptor Information
>6plf Chain A (length=305) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NLRKVLISDSLDPCCRKILQDGGLQVVEKQNLSKEELIAELQDCEGLIVR
SATKVTADVINAAEKLQVVGRAGTGVDNVDLEAATRKGILVMNTPNGNSL
SAAELTCGMIMCLARQIPQATASMKDGKWERKKFMGTELNGKTLGILGLG
RIGREVATRMQSFGMKTIGYDPIISPEVSASFGVQQLPLEEIWPLCDFIT
VHTPLLPSTTGLLNDNTFAQCKKGVRVVNCARGGIVDEGALLRALQSGQC
AGAALDVFTEEPPRDRALVDHENVISCPHLGASTKEAQSRCGEEIAVQFV
DMVKG
Ligand information
Ligand IDONV
InChIInChI=1S/C22H20ClN3O7/c23-15-5-13-6-17(25-16(13)7-19(15)32-10-14-8-24-22(31)33-14)20(28)26-18(9-27)11-1-3-12(4-2-11)21(29)30/h1-7,14,18,25,27H,8-10H2,(H,24,31)(H,26,28)(H,29,30)/t14-,18+/m0/s1
InChIKeyHSLVBDMYOQHSSR-KBXCAEBGSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7c1cc(ccc1C(CO)NC(=O)c2cc3cc(c(cc3[nH]2)OCC4CNC(=O)O4)Cl)C(=O)O
CACTVS 3.385OC[CH](NC(=O)c1[nH]c2cc(OC[CH]3CNC(=O)O3)c(Cl)cc2c1)c4ccc(cc4)C(O)=O
CACTVS 3.385OC[C@@H](NC(=O)c1[nH]c2cc(OC[C@@H]3CNC(=O)O3)c(Cl)cc2c1)c4ccc(cc4)C(O)=O
OpenEye OEToolkits 2.0.7c1cc(ccc1[C@@H](CO)NC(=O)c2cc3cc(c(cc3[nH]2)OC[C@@H]4CNC(=O)O4)Cl)C(=O)O
ACDLabs 12.01C4(COc1c(Cl)cc3c(c1)nc(C(NC(c2ccc(C(=O)O)cc2)CO)=O)c3)CNC(O4)=O
FormulaC22 H20 Cl N3 O7
Name4-{(1S)-1-[(5-chloro-6-{[(5S)-2-oxo-1,3-oxazolidin-5-yl]methoxy}-1H-indole-2-carbonyl)amino]-2-hydroxyethyl}benzoic acid
ChEMBLCHEMBL4554985
DrugBank
ZINC
PDB chain6plf 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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PDB6plf Inhibition of 3-phosphoglycerate dehydrogenase (PHGDH) by indole amides abrogates de novo serine synthesis in cancer cells.
Resolution1.7 Å
Binding residue
(original residue number in PDB)		Y174 D175 P176 L193 H206 T207 P208 L216
Binding residue
(residue number reindexed from 1)		Y170 D171 P172 L189 H202 T203 P204 L212
Annotation score1
Binding affinityMOAD: ic50=0.238uM
PDBbind-CN: -logKd/Ki=6.67,Ki=214nM
BindingDB: IC50=238nM,Ki=214nM
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:6plf, PDBe:6plf, PDBj:6plf
PDBsum6plf
PubMed31327531
UniProtO43175|SERA_HUMAN D-3-phosphoglycerate dehydrogenase (Gene Name=PHGDH)

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