Structure of PDB 1i41 Chain C Binding Site BS02

Receptor Information
>1i41 Chain C (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)		S137 G138 M139 Y163 E207 D236 S258 T260 K261 S388 F389 S403 R423
Binding residue
(residue number reindexed from 1)		S88 G89 M90 Y114 E158 D187 S209 T211 K212 S339 F340 S354 R374
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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