Structure of PDB 1i41 Chain A Binding Site BS02

Receptor Information
>1i41 Chain A (length=396) Species: 4097 (Nicotiana tabacum) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
YASFLNSDGSVAIHAGERLGRGIVTDAITTPVVNTSAYFFNKTSELIDFK
EKRRASFEYGRYGNPTTVVLEEKISALEGAESTLLMASGMCASTVMLLAL
VPAGGHIVTTTDCYRKTRIFIETILPKMGITATVIDPADVGALELALNQK
KVNLFFTESPTNPFLRCVDIELVSKLCHEKGALVCIDGTFATPLNQKALA
LGADLVLHSATKFLGGHNDVLAGCISGPLKLVSEIRNLHHILGGALNPNA
AYLIIRGMKTLHLRVQQQNSTALRMAEILEAHPKVRHVYYPGLQSHPEHH
IAKKQMTGFGGAVSFEVDGDLLTTAKFVDALKIPYIAPSFGGCESIVDQP
AIMSYWDLSQSDRAKYGIMDNLVRFSFGVEDFDDLKADILQALDSI
Ligand information
Ligand IDHEN
InChIInChI=1S/C13H18N2O10P2/c1-8-12(16)10(9(5-14-8)7-25-27(22,23)24)6-15-11(13(17)18)3-2-4-26(19,20)21/h2-3,5,16H,4,6-7H2,1H3,(H,17,18)(H2,19,20,21)(H2,22,23,24)/b3-2+,15-11+
InChIKeyVKWJKURKEYQKKW-ZCOJICPHSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Cc1ncc(CO[P](O)(O)=O)c(CN=C(\C=C\C[P](O)(O)=O)C(O)=O)c1O
OpenEye OEToolkits 1.5.0Cc1c(c(c(cn1)COP(=O)(O)O)C/N=C(\C=C\CP(=O)(O)O)/C(=O)O)O
CACTVS 3.341Cc1ncc(CO[P](O)(O)=O)c(CN=C(C=CC[P](O)(O)=O)C(O)=O)c1O
ACDLabs 10.04O=P(O)(O)C/C=C/C(=N\Cc1c(cnc(c1O)C)COP(=O)(O)O)C(=O)O
OpenEye OEToolkits 1.5.0Cc1c(c(c(cn1)COP(=O)(O)O)CN=C(C=CCP(=O)(O)O)C(=O)O)O
FormulaC13 H18 N2 O10 P2
Name2-[(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL)-IMINO]-5-PHOSPHONO-PENT-3-ENOIC ACID
ChEMBL
DrugBankDB02328
ZINCZINC000103544596
PDB chain1i41 Chain C Residue 502 [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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PDB1i41 Crystal structures of cystathionine gamma-synthase inhibitor complexes rationalize the increased affinity of a novel inhibitor.
Resolution3.2 Å
Binding residue
(original residue number in PDB)		E107 Y108 R110 Y111
Binding residue
(residue number reindexed from 1)		E58 Y59 R61 Y62
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=4.57,Ki=27uM
Enzymatic activity
Catalytic site (original residue number in PDB) R110 Y163 D236 K261
Catalytic site (residue number reindexed from 1) R61 Y114 D187 K212
Enzyme Commision number 4.2.99.9: Transferred entry: 2.5.1.48.
Gene Ontology
Molecular Function
GO:0003962 cystathionine gamma-synthase activity
GO:0030170 pyridoxal phosphate binding
Biological Process
GO:0009086 methionine biosynthetic process
GO:0019346 transsulfuration

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:1i41, PDBe:1i41, PDBj:1i41
PDBsum1i41
PubMed11518531
UniProtQ9ZPL5

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