Structure of PDB 6jid Chain A Binding Site BS01

Receptor Information
>6jid Chain A (length=294) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EAVVISGRKLAQQIKQEVRQEVEEWVASGNKRPHLSVILVGENPASHSYV
LNKTRAAAVVGINSETIMKPASISEEELLNLINKLNNDDNVDGLLVQLPL
PEHIDERRICNAVSPDKDVDGFHVINVGRMCLDQYSMLPATPWGVWEIIK
RTGIPTLGKNVVVAGRSKNVGMPIAMLLHTDGAHERPGGDATVTISHRYT
PKEQLKKHTILADIVISAAGIPNLITADMIKEGAAVIDVGINRVHDKPKL
VGDVDFEGVRQKAGYITPVPGGVGPMTVAMLMKNTIIAAKKVLR
Ligand information
Ligand IDBQC
InChIInChI=1S/C21H18N4O4S/c26-20-16-11-25(9-8-18(16)22-19(23-20)13-4-2-1-3-5-13)21(27)14-6-7-17-15(10-14)12-30(28,29)24-17/h1-7,10,24H,8-9,11-12H2,(H,22,23,26)
InChIKeyXRENRYGQQDHQAY-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6c1ccc(cc1)C2=NC(=O)C3=C(N2)CCN(C3)C(=O)c4ccc5c(c4)CS(=O)(=O)N5
ACDLabs 12.01S2(=O)(Nc1ccc(cc1C2)C(=O)N3CCC4=C(C3)C(=O)N=C(N4)c5ccccc5)=O
CACTVS 3.385O=C1N=C(NC2=C1CN(CC2)C(=O)c3ccc4N[S](=O)(=O)Cc4c3)c5ccccc5
FormulaC21 H18 N4 O4 S
Name5-(4-oxo-2-phenyl-1,5,7,8-tetrahydropyrido[4,3-d]pyrimidine-6(4H)-carbonyl)-1,3-dihydro-2H-2lambda~6~,1-benzothiazole-2,2-dione
ChEMBLCHEMBL4520035
DrugBank
ZINC
PDB chain6jid 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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PDB6jid Structure-Based Design and Synthesis of an Isozyme-Selective MTHFD2 Inhibitor with a Tricyclic Coumarin Scaffold.
Resolution2.5 Å
Binding residue
(original residue number in PDB)		Y84 N87 K88 Q132 I276 P309 G313 P314 V317
Binding residue
(residue number reindexed from 1)		Y49 N52 K53 Q97 I241 P270 G274 P275 V278
Annotation score1
Binding affinityMOAD: ic50=8.3uM
PDBbind-CN: -logKd/Ki=5.08,IC50=8.3uM
Enzymatic activity
Enzyme Commision number 1.5.1.15: methylenetetrahydrofolate dehydrogenase (NAD(+)).
3.5.4.9: methenyltetrahydrofolate cyclohydrolase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0004488 methylenetetrahydrofolate dehydrogenase (NADP+) activity

View graph for
Molecular Function
External links
PDB RCSB:6jid, PDBe:6jid, PDBj:6jid
PDBsum6jid
PubMed31223444
UniProtP13995|MTDC_HUMAN Bifunctional methylenetetrahydrofolate dehydrogenase/cyclohydrolase, mitochondrial (Gene Name=MTHFD2)

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