Structure of PDB 4wcm Chain A Binding Site BS04

Receptor Information

>4wcm Chain A (length=415) Species: 563041 (Helicobacter pylori G27)

MEMIEKAPTDLEDRDKAPHLLLLAGIHGDEPGGFNATNLFLMHYSVLKGL
VEVVPVLNKPSMLRNHRGLYGDMNRKFAALDKKDPEYPTIQEIKSLIAKP
NIDAVLHLHDGGGYYRPVYVDAMLNPKRWGNCFIIDQDEVKGAKFPNLLA
FANNTIESINAHLLHPIEEYHLKNTRTAQGDTEMQKALTFYAINQKKSAF
ANEASKELPLASRVFYHLQAIEGLLNQLNIPFKRDFELNPSSVHALINDK
SLWAKISSLPKIPLFNLRPRLNHFPLPHNTKIPQIPIESNAYIVGLVKNK
QEVFLKYGNKLMTRLSPFYIEFDPSLEEVKMQIDNKDQMVKIGSVVEVKE
SFYIHAMDNIRANVIGFSVKPNEAGYTIRFKDFQKRFSLDKQERIYRIEF
YKNNAFSGMILVKFV

Ligand information

• Ligand ID: API
• InChI: InChI=1S/C7H14N2O4/c8-4(6(10)11)2-1-3-5(9)7(12)13/h4-5H,1-3,8-9H2,(H,10,11)(H,12,13)/t4-,5+
• InChIKey: GMKMEZVLHJARHF-SYDPRGILSA-N
• SMILES:
  CACTVS 3.370: N[CH](CCC[CH](N)C(O)=O)C(O)=O
  OpenEye OEToolkits 1.7.2: C(C[C@H](C(=O)O)N)C[C@@H](C(=O)O)N
  OpenEye OEToolkits 1.7.2: C(CC(C(=O)O)N)CC(C(=O)O)N
  CACTVS 3.370: N[C@@H](CCC[C@@H](N)C(O)=O)C(O)=O
  ACDLabs 12.01: O=C(O)C(N)CCCC(C(=O)O)N
• Formula: C7 H14 N2 O4
• Name: 2,6-DIAMINOPIMELIC ACID
• ChEMBL: CHEMBL415306
• ZINC: ZINC000001532722
• PDB chain: 4wcm Chain A Residue 543

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4wcm Helical Shape of Helicobacter pylori Requires an Atypical Glutamine as a Zinc Ligand in the Carboxypeptidase Csd4.
• Resolution: 1.75 Å
• Binding residue (original residue number in PDB): N93 R94 H126 H128 W148 M203 T208 A220 E222
• Binding residue (residue number reindexed from 1): N74 R75 H107 H109 W129 M184 T189 A201 E203
• Annotation score: 1

Gene Ontology

Molecular Function

• GO:0046872 metal ion binding

External links

• PDB: RCSB:4wcm, PDBe:4wcm, PDBj:4wcm
• PDBsum: 4wcm
• PubMed: 25505267
• UniProt: B5ZAD9