Structure of PDB 6s4f Chain B Binding Site BS01

Receptor Information
>6s4f Chain B (length=298) 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
PKEQLKKHTILADIVISAAGIPNLITADMIKEGAAVIDVGINRVHDPVTA
KPKLVGDVDFEGVRQKAGYITPVPGGVGPMTVAMLMKNTIIAAKKVLR
Ligand information
Ligand IDKUN
InChIInChI=1S/C17H18FN7O7/c18-8-3-6(22-10(26)4-7-13(19)24-17(20)25-14(7)29)5-21-12(8)15(30)23-9(16(31)32)1-2-11(27)28/h3,5,9H,1-2,4H2,(H,22,26)(H,23,30)(H,27,28)(H,31,32)(H5,19,20,24,25,29)/t9-/m0/s1
InChIKeyALGPVOJFIGPPPX-VIFPVBQESA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7c1c(cnc(c1F)C(=O)NC(CCC(=O)O)C(=O)O)NC(=O)CC2=C(NC(=NC2=O)N)N
CACTVS 3.385NC1=NC(=O)C(=C(N)N1)CC(=O)Nc2cnc(c(F)c2)C(=O)N[CH](CCC(O)=O)C(O)=O
OpenEye OEToolkits 2.0.7c1c(cnc(c1F)C(=O)N[C@@H](CCC(=O)O)C(=O)O)NC(=O)CC2=C(NC(=NC2=O)N)N
CACTVS 3.385NC1=NC(=O)C(=C(N)N1)CC(=O)Nc2cnc(c(F)c2)C(=O)N[C@@H](CCC(O)=O)C(O)=O
FormulaC17 H18 F N7 O7
Name(E,4S)-4-[[5-[2-[2,6-bis(azanyl)-4-oxidanylidene-1H-pyrimidin-5-yl]ethanoylamino]-3-fluoranyl-pyridin-2-yl]carbonylamino]pent-2-enedioic acid;
TH9619
ChEMBL
DrugBank
ZINC
PDB chain6s4f 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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PDB6s4f Pharmacological targeting of MTHFD2 suppresses acute myeloid leukemia by inducing thymidine depletion and replication stress.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		S83 Y84 N87 K88 V131 Q132 L133 D155 F157 I276 P309 G310 G313 P314 V317
Binding residue
(residue number reindexed from 1)		S48 Y49 N52 K53 V96 Q97 L98 D120 F122 I241 P274 G275 G278 P279 V282
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) S81 K88 Q132 D155
Catalytic site (residue number reindexed from 1) S46 K53 Q97 D120
Enzyme Commision number 1.5.1.15: methylenetetrahydrofolate dehydrogenase (NAD(+)).
3.5.4.9: methenyltetrahydrofolate cyclohydrolase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0003824 catalytic activity
GO:0004477 methenyltetrahydrofolate cyclohydrolase activity
GO:0004487 methylenetetrahydrofolate dehydrogenase (NAD+) activity
GO:0004488 methylenetetrahydrofolate dehydrogenase (NADP+) activity
GO:0005515 protein binding
GO:0016491 oxidoreductase activity
GO:0016787 hydrolase activity
GO:0042301 phosphate ion binding
Biological Process
GO:0006730 one-carbon metabolic process
GO:0035999 tetrahydrofolate interconversion
GO:0046653 tetrahydrofolate metabolic process
GO:0046655 folic acid metabolic process
Cellular Component
GO:0005615 extracellular space
GO:0005739 mitochondrion
GO:0005759 mitochondrial matrix

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6s4f, PDBe:6s4f, PDBj:6s4f
PDBsum6s4f
PubMed35228749
UniProtP13995|MTDC_HUMAN Bifunctional methylenetetrahydrofolate dehydrogenase/cyclohydrolase, mitochondrial (Gene Name=MTHFD2)

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