Structure of PDB 5tc4 Chain A Binding Site BS01

Receptor Information
>5tc4 Chain A (length=292) 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
GDVDFEGVRQKAGYITPVPGGVGPMTVAMLMKNTIIAAKKVL
Ligand information
Ligand IDNAD
InChIInChI=1S/C21H27N7O14P2/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(32)14(30)11(41-21)6-39-44(36,37)42-43(34,35)38-5-10-13(29)15(31)20(40-10)27-3-1-2-9(4-27)18(23)33/h1-4,7-8,10-11,13-16,20-21,29-32H,5-6H2,(H5-,22,23,24,25,33,34,35,36,37)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKeyBAWFJGJZGIEFAR-NNYOXOHSSA-N
SMILES
SoftwareSMILES
CACTVS 3.341NC(=O)c1ccc[n+](c1)[C@@H]2O[C@H](CO[P]([O-])(=O)O[P@](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
OpenEye OEToolkits 1.5.0c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)N
CACTVS 3.341NC(=O)c1ccc[n+](c1)[CH]2O[CH](CO[P]([O-])(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
OpenEye OEToolkits 1.5.0c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)([O-])O[P@@](=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)N
FormulaC21 H27 N7 O14 P2
NameNICOTINAMIDE-ADENINE-DINUCLEOTIDE
ChEMBLCHEMBL1234613
DrugBankDB14128
ZINC
PDB chain5tc4 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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PDB5tc4 Crystal Structure of the Emerging Cancer Target MTHFD2 in Complex with a Substrate-Based Inhibitor.
Resolution1.89 Å
Binding residue
(original residue number in PDB)		T176 G200 R201 S202 N204 V205 H232 R233 A253 A254 I256 V274 G275 I276 G313 T316
Binding residue
(residue number reindexed from 1)		T141 G165 R166 S167 N169 V170 H197 R198 A218 A219 I221 V239 G240 I241 G273 T276
Annotation score4
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:5tc4, PDBe:5tc4, PDBj:5tc4
PDBsum5tc4
PubMed27899380
UniProtP13995|MTDC_HUMAN Bifunctional methylenetetrahydrofolate dehydrogenase/cyclohydrolase, mitochondrial (Gene Name=MTHFD2)

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