Structure of PDB 6kg2 Chain A Binding Site BS01

Receptor Information
>6kg2 Chain A (length=293) 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
PKEQLKKHTILADIVISAAGIPNLITADMIKEGAAVIDVGINRVHKPKLV
GDVDFEGVRQKAGYITPVPGGVGPMTVAMLMKNTIIAAKKVLR
Ligand information
Ligand IDD8C
InChIInChI=1S/C26H29ClN4O5S/c1-16-23(30-12-10-29(2)11-13-30)7-5-19-18-8-9-31(15-20(18)26(33)36-24(16)19)25(32)17-4-6-22(21(27)14-17)28-37(3,34)35/h4-7,14,28H,8-13,15H2,1-3H3
InChIKeyDHJUEJALVPLBJH-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CN1CCN(CC1)c2ccc3C4=C(CN(CC4)C(=O)c5ccc(N[S](C)(=O)=O)c(Cl)c5)C(=O)Oc3c2C
OpenEye OEToolkits 2.0.7Cc1c(ccc2c1OC(=O)C3=C2CCN(C3)C(=O)c4ccc(c(c4)Cl)NS(=O)(=O)C)N5CCN(CC5)C
FormulaC26 H29 Cl N4 O5 S
NameN-[2-chloranyl-4-[[7-methyl-8-(4-methylpiperazin-1-yl)-5-oxidanylidene-2,4-dihydro-1H-chromeno[3,4-c]pyridin-3-yl]carbonyl]phenyl]methanesulfonamide
ChEMBLCHEMBL4546647
DrugBank
ZINC
PDB chain6kg2 Chain A Residue 500 [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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PDB6kg2 Discovery of a Potent, Selective, and Orally Available MTHFD2 Inhibitor (DS18561882) with in Vivo Antitumor Activity.
Resolution2.25 Å
Binding residue
(original residue number in PDB)		Y84 N87 K88 Q132 L133 P309 G310 G313 P314 V317
Binding residue
(residue number reindexed from 1)		Y49 N52 K53 Q97 L98 P269 G270 G273 P274 V277
Annotation score1
Binding affinityMOAD: ic50=0.048uM
BindingDB: IC50=48nM
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:6kg2, PDBe:6kg2, PDBj:6kg2
PDBsum6kg2
PubMed31638799
UniProtP13995|MTDC_HUMAN Bifunctional methylenetetrahydrofolate dehydrogenase/cyclohydrolase, mitochondrial (Gene Name=MTHFD2)

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