Structure of PDB 1dib Chain A Binding Site BS02

Receptor Information
>1dib Chain A (length=285) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
APAEILNGKEISAQIRARLKNQVTQLKEQVPGFTPRLAILQVGNRDDSNL
YINVKLKAAEEIGIKATHIKLPRTTTESEVMKYITSLNEDSTVHGFLVQL
PLDSENSINTEEVINAIAPEKDVDGLTSINAGRLARGDLNDCFIPCTPKG
CLELIKETGVPIAGRHAVVVGRSKIVGAPMHDLLLWNNATVTTCHSKTAH
LDEEVNKGDILVVATGQPEMVKGEWIKPGAIVIDCGINYKVVGDVAYDEA
KERASFITPVPGGVGPMTVAMLMQSTVESAKRFLE
Ligand information
Ligand IDL34
InChIInChI=1S/C20H21N7O7/c21-19-24-15-14(17(31)25-19)27-11(7-22-15)8-26(20(27)34)10-3-1-9(2-4-10)16(30)23-12(18(32)33)5-6-13(28)29/h1-4,11-12H,5-8H2,(H,23,30)(H,28,29)(H,32,33)(H4,21,22,24,25,31)/t11-,12+/m1/s1
InChIKeyJSNFRYBHBVDHSG-NEPJUHHUSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C(O)C(NC(=O)c4ccc(N3C(=O)N2c1c(nc(nc1O)N)NCC2C3)cc4)CCC(=O)O
OpenEye OEToolkits 1.5.0c1cc(ccc1C(=O)N[C@@H](CCC(=O)O)C(=O)O)N2C[C@H]3CNc4c(c(nc(n4)N)O)N3C2=O
CACTVS 3.341Nc1nc(O)c2N3[CH](CNc2n1)CN(C3=O)c4ccc(cc4)C(=O)N[CH](CCC(O)=O)C(O)=O
OpenEye OEToolkits 1.5.0c1cc(ccc1C(=O)NC(CCC(=O)O)C(=O)O)N2CC3CNc4c(c(nc(n4)N)O)N3C2=O
CACTVS 3.341Nc1nc(O)c2N3[C@H](CNc2n1)CN(C3=O)c4ccc(cc4)C(=O)N[C@@H](CCC(O)=O)C(O)=O
FormulaC20 H21 N7 O7
Name4-(7-AMINO-9-HYDROXY-1-OXO-3,3A,4,5-TETRAHYDRO-2,5,6,8,9B-PENTAAZA-CYCLOPENTA[A]NAPHTHALEN-2-YL)-PHENYLCARBONYL-GLUTAMI C ACID;
LY345899
ChEMBLCHEMBL1233930
DrugBank
ZINC
PDB chain1dib Chain A Residue 3001 [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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PDB1dib Structures of three inhibitor complexes provide insight into the reaction mechanism of the human methylenetetrahydrofolate dehydrogenase/cyclohydrolase.
Resolution2.7 Å
Binding residue
(original residue number in PDB)		Y52 K56 L101 D125 G273 G276 P277 T279 V280
Binding residue
(residue number reindexed from 1)		Y51 K55 L100 D124 G262 G265 P266 T268 V269
Annotation score3
Binding affinityBindingDB: IC50=96nM
Enzymatic activity
Enzyme Commision number 1.5.1.5: methylenetetrahydrofolate dehydrogenase (NADP(+)).
3.5.4.9: methenyltetrahydrofolate cyclohydrolase.
6.3.4.3: formate--tetrahydrofolate ligase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0004488 methylenetetrahydrofolate dehydrogenase (NADP+) activity

View graph for
Molecular Function
External links
PDB RCSB:1dib, PDBe:1dib, PDBj:1dib
PDBsum1dib
PubMed10828945
UniProtP11586|C1TC_HUMAN C-1-tetrahydrofolate synthase, cytoplasmic (Gene Name=MTHFD1)

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