Structure of PDB 6jib Chain B Binding Site BS01

Receptor Information
>6jib Chain B (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 IDBQF
InChIInChI=1S/C20H15NO5/c22-18(12-5-7-13(8-6-12)19(23)24)21-10-9-14-15-3-1-2-4-17(15)26-20(25)16(14)11-21/h1-8H,9-11H2,(H,23,24)
InChIKeyOXUKTNZACAKVRG-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385OC(=O)c1ccc(cc1)C(=O)N2CCC3=C(C2)C(=O)Oc4ccccc34
OpenEye OEToolkits 2.0.6c1ccc2c(c1)C3=C(CN(CC3)C(=O)c4ccc(cc4)C(=O)O)C(=O)O2
ACDLabs 12.01C(O)(c1ccc(cc1)C(=O)N4CC3=C(c2c(cccc2)OC3=O)CC4)=O
FormulaC20 H15 N O5
Name4-(5-oxo-1,5-dihydro-2H-[1]benzopyrano[3,4-c]pyridine-3(4H)-carbonyl)benzoic acid
ChEMBLCHEMBL4474283
DrugBank
ZINC
PDB chain6jib Chain B 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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PDB6jib Structure-Based Design and Synthesis of an Isozyme-Selective MTHFD2 Inhibitor with a Tricyclic Coumarin Scaffold.
Resolution2.25 Å
Binding residue
(original residue number in PDB)		Y84 N87 K88 Q132 P309 G310 G313 P314 V317
Binding residue
(residue number reindexed from 1)		Y49 N52 K53 Q97 P270 G271 G274 P275 V278
Annotation score1
Binding affinityMOAD: ic50=1.6uM
BindingDB: IC50=1600nM
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:6jib, PDBe:6jib, PDBj:6jib
PDBsum6jib
PubMed31223444
UniProtP13995|MTDC_HUMAN Bifunctional methylenetetrahydrofolate dehydrogenase/cyclohydrolase, mitochondrial (Gene Name=MTHFD2)

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