Structure of PDB 6vnd Chain A Binding Site BS01

Receptor Information
>6vnd Chain A (length=365) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ATGDERFYAEHLMPTLQGLLDPESAHRLAVRFTSLGLLPRARFQDSDMLE
VRVLGHKFRNPVGIAAGFDKHGEAVDGLYKMGFGFVEIGSVTPKPQEGNP
RPRVFRLPEDQAVINRYGFNSHGLSVVEHRLRARQQKQAKLTEDGLPLGV
NLGKNKTSVDAAEDYAEGVRVLGPLADYLVVNVSSPNTAGLRSLQGKAEL
RRLLTKVLQERDGLRRVHRPAVLVKIAPDLTSQDKEDIASVVKELGIDGL
IVTNTTVSRPAGLQGALRSETGGLSGKPLRDLSTQTIREMYALTQGRVPI
IGVGGVSSGQDALEKIRAGASLVQLYTALTFWGPPVVGKVKRELEALLKE
QGFGGVTDAIGADHR
Ligand information
Ligand IDR4P
InChIInChI=1S/C21H17N3O2/c1-13-5-3-4-6-17(13)15-9-7-14(8-10-15)16-11-18(21(25)26)20-19(12-16)22-23-24(20)2/h3-12H,1-2H3,(H,25,26)
InChIKeyGSBZRCGZLMBSNY-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7Cc1ccccc1c2ccc(cc2)c3cc(c4c(c3)nnn4C)C(=O)O
CACTVS 3.385Cn1nnc2cc(cc(C(O)=O)c12)c3ccc(cc3)c4ccccc4C
ACDLabs 12.01c1(cc(cc2c1n(C)nn2)c3ccc(cc3)c4c(cccc4)C)C(=O)O
FormulaC21 H17 N3 O2
Name1-methyl-5-(2'-methyl[1,1'-biphenyl]-4-yl)-1H-benzotriazole-7-carboxylic acid
ChEMBL
DrugBank
ZINC
PDB chain6vnd Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6vnd Selective Vulnerability to Pyrimidine Starvation in Hematologic Malignancies Revealed by AG-636, a Novel Clinical-Stage Inhibitor of Dihydroorotate Dehydrogenase.
Resolution1.97 Å
Binding residue
(original residue number in PDB)		M42 Q46 P51 A54 H55 A58 L67 R135 Y355 T359 P363
Binding residue
(residue number reindexed from 1)		M13 Q17 P22 A25 H26 A29 L38 R106 Y326 T330 P334
Annotation score1
Binding affinityMOAD: ic50=17nM
Enzymatic activity
Catalytic site (original residue number in PDB) N144 F148 S214 N216 T217 K254 N283
Catalytic site (residue number reindexed from 1) N115 F119 S185 N187 T188 K225 N254
Enzyme Commision number 1.3.5.2: dihydroorotate dehydrogenase (quinone).
Gene Ontology
Molecular Function
GO:0004151 dihydroorotase activity
GO:0004152 dihydroorotate dehydrogenase activity
GO:0005515 protein binding
GO:0016491 oxidoreductase activity
GO:0016627 oxidoreductase activity, acting on the CH-CH group of donors
GO:0106430 dihydroorotate dehydrogenase (quinone) activity
Biological Process
GO:0006207 'de novo' pyrimidine nucleobase biosynthetic process
GO:0006221 pyrimidine nucleotide biosynthetic process
GO:0006225 UDP biosynthetic process
GO:0009220 pyrimidine ribonucleotide biosynthetic process
GO:0044205 'de novo' UMP biosynthetic process
Cellular Component
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005743 mitochondrial inner membrane
GO:0005829 cytosol
GO:0016020 membrane

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6vnd, PDBe:6vnd, PDBj:6vnd
PDBsum6vnd
PubMed33082276
UniProtQ02127|PYRD_HUMAN Dihydroorotate dehydrogenase (quinone), mitochondrial (Gene Name=DHODH)

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