Structure of PDB 6rj5 Chain B Binding Site BS01

Receptor Information
>6rj5 Chain B (length=302) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LRKVLISDSLDPCCRKILQDGGLQVVEKQNLSKEELIAELQDCEGLIVRS
ATKVTADVINAAEKLQVVGRAGTGVDNVDLEAATRKGILVMNTPNGNSLS
AAELTCGMIMCLARQIPQATASMKDGKWERKKFMGTELNGKTLGILGLGR
IGREVATRMQSFGMKTIGYDPIISPEVSASFGVQQLPLEEIWPLCDFITV
HTPLLPSTTGLLNDNTFAQCKKGVRVVNCARGGIVDEGALLRALQSGQCA
GAALDVFTEEPPRDRALVDHENVISCPHLGASTKEAQSRCGEEIAVQFVD
MV
Ligand information
Ligand IDK5N
InChIInChI=1S/C21H22N4O4S/c1-14(15-9-11-17(12-10-15)20(26)24-30(3,28)29)22-21(27)19-13-18(23-25(19)2)16-7-5-4-6-8-16/h4-14H,1-3H3,(H,22,27)(H,24,26)/t14-/m1/s1
InChIKeyMRQUJSLINQBOAA-CQSZACIVSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7C[C@H](c1ccc(cc1)C(=O)NS(=O)(=O)C)NC(=O)c2cc(nn2C)c3ccccc3
CACTVS 3.385C[CH](NC(=O)c1cc(nn1C)c2ccccc2)c3ccc(cc3)C(=O)N[S](C)(=O)=O
CACTVS 3.385C[C@@H](NC(=O)c1cc(nn1C)c2ccccc2)c3ccc(cc3)C(=O)N[S](C)(=O)=O
OpenEye OEToolkits 2.0.7CC(c1ccc(cc1)C(=O)NS(=O)(=O)C)NC(=O)c2cc(nn2C)c3ccccc3
FormulaC21 H22 N4 O4 S
Name2-methyl-~{N}-[(1~{R})-1-[4-(methylsulfonylcarbamoyl)phenyl]ethyl]-5-phenyl-pyrazole-3-carboxamide
ChEMBLCHEMBL4528650
DrugBank
ZINC
PDB chain6rj5 Chain B Residue 402 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB6rj5 Intracellular Trapping of the Selective Phosphoglycerate Dehydrogenase (PHGDH) InhibitorBI-4924Disrupts Serine Biosynthesis.
Resolution1.89 Å
Binding residue
(original residue number in PDB)		P98 G153 Y173 D174 P175 I176 H205 T206 P207 L215
Binding residue
(residue number reindexed from 1)		P94 G149 Y169 D170 P171 I172 H201 T202 P203 L211
Annotation score1
Binding affinityMOAD: ic50=0.3uM
BindingDB: IC50=300nM
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:6rj5, PDBe:6rj5, PDBj:6rj5
PDBsum6rj5
PubMed31365252
UniProtO43175|SERA_HUMAN D-3-phosphoglycerate dehydrogenase (Gene Name=PHGDH)

[Back to BioLiP]