Structure of PDB 4zyu Chain A Binding Site BS02

Receptor Information

>4zyu Chain A (length=200) Species: 9606 (Homo sapiens)

ARVAVLISGTGSNLQALIDSTREPNSSAQIDIVISNKAAVAGLDKAERAG
IPTRVINHKLYKNRVEFDSAIDLVLEEFSIDIVCLAGFMRILSGPFVQKW
NGKMLNIHPSLLPSFKGSNAHEQALETGVTVTGCTVHFVAEDVDAGQIIL
QEAVPVKRGDTVATLSERVKLAEHKIFPAALQLVASGTVQLGENGKICWV

Ligand information

• Ligand ID: 3YA
• InChI: InChI=1S/C22H24N4O6S/c23-22-25-19(30)15-11-14(33-20(15)26-22)4-2-1-3-12-5-7-13(8-6-12)18(29)24-16(21(31)32)9-10-17(27)28/h5-8,11,16H,1-4,9-10H2,(H,24,29)(H,27,28)(H,31,32)(H3,23,25,26,30)/t16-/m0/s1
• InChIKey: KVBZUTNKUVNMNN-INIZCTEOSA-N
• SMILES:
  CACTVS 3.385: NC1=NC(=O)c2cc(CCCCc3ccc(cc3)C(=O)N[C@@H](CCC(O)=O)C(O)=O)sc2N1
  OpenEye OEToolkits 1.9.2: c1cc(ccc1CCCCc2cc3c(s2)NC(=NC3=O)N)C(=O)NC(CCC(=O)O)C(=O)O
  ACDLabs 12.01: c1cc(ccc1C(NC(CCC(O)=O)C(O)=O)=O)CCCCc2sc3NC(=NC(=O)c3c2)N
  OpenEye OEToolkits 1.9.2: c1cc(ccc1CCCCc2cc3c(s2)NC(=NC3=O)N)C(=O)N[C@@H](CCC(=O)O)C(=O)O
  CACTVS 3.385: NC1=NC(=O)c2cc(CCCCc3ccc(cc3)C(=O)N[CH](CCC(O)=O)C(O)=O)sc2N1
• Formula: C22 H24 N4 O6 S
• Name: N-{4-[4-(2-amino-4-oxo-1,4-dihydrothieno[2,3-d]pyrimidin-6-yl)butyl]benzoyl}-L-glutamic acid
• ChEMBL: CHEMBL491104
• ZINC: ZINC000045506339
• PDB chain: 4zyu Chain A Residue 1102

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4zyu Structural and Enzymatic Analysis of Tumor-Targeted Antifolates That Inhibit Glycinamide Ribonucleotide Formyltransferase.
• Resolution: 1.95 Å
• Binding residue (original residue number in PDB): L892 F895 M896 R897 I898 L899 N913 V946 A947 V950
• Binding residue (residue number reindexed from 1): L85 F88 M89 R90 I91 L92 N106 V139 A140 V143
• Annotation score: 2
• Binding affinity: MOAD: Ki=1067nM
  PDBbind-CN: -logKd/Ki=5.97,Ki=1067nM

Enzymatic activity

• Catalytic site (original residue number in PDB): N913 H915 T942 D951
• Catalytic site (residue number reindexed from 1): N106 H108 T135 D144
• Enzyme Commision number: 2.1.2.2: phosphoribosylglycinamide formyltransferase 1.
  6.3.3.1: phosphoribosylformylglycinamidine cyclo-ligase.
  6.3.4.13: phosphoribosylamine--glycine ligase.

Gene Ontology

Molecular Function

• GO:0004644 phosphoribosylglycinamide formyltransferase activity

Biological Process

• GO:0006189 'de novo' IMP biosynthetic process
• GO:0009058 biosynthetic process

External links

• PDB: RCSB:4zyu, PDBe:4zyu, PDBj:4zyu
• PDBsum: 4zyu
• PubMed: 27439469
• UniProt: P22102|PUR2_HUMAN Trifunctional purine biosynthetic protein adenosine-3 (Gene Name=GART)