Structure of PDB 4zyz Chain A Binding Site BS02

Receptor Information
>4zyz Chain A (length=200) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ARVAVLISGTGSNLQALIDSTREPNSSAQIDIVISNKAAVAGLDKAERAG
IPTRVINHKLYKNRVEFDSAIDLVLEEFSIDIVCLAGFMRILSGPFVQKW
NGKMLNIHPSLLPSFKGSNAHEQALETGVTVTGCTVHFVAEDVDAGQIIL
QEAVPVKRGDTVATLSERVKLAEHKIFPAALQLVASGTVQLGENGKICWV
Ligand information
Ligand ID3YD
InChIInChI=1S/C18H25N5O6/c19-18-22-15-11(16(27)23-18)9-10(20-15)5-3-1-2-4-6-13(24)21-12(17(28)29)7-8-14(25)26/h9,12H,1-8H2,(H,21,24)(H,25,26)(H,28,29)(H4,19,20,22,23,27)/t12-/m0/s1
InChIKeyYFTJOYZLYVUUOD-LBPRGKRZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2c1c([nH]c2c1C(=O)NC(=N2)N)CCCCCCC(=O)NC(CCC(=O)O)C(=O)O
CACTVS 3.385NC1=Nc2[nH]c(CCCCCCC(=O)N[CH](CCC(O)=O)C(O)=O)cc2C(=O)N1
ACDLabs 12.01N1=C(NC(=O)c2cc(nc12)CCCCCCC(=O)NC(C(=O)O)CCC(O)=O)N
OpenEye OEToolkits 1.9.2c1c([nH]c2c1C(=O)NC(=N2)N)CCCCCCC(=O)N[C@@H](CCC(=O)O)C(=O)O
CACTVS 3.385NC1=Nc2[nH]c(CCCCCCC(=O)N[C@@H](CCC(O)=O)C(O)=O)cc2C(=O)N1
FormulaC18 H25 N5 O6
Name(S)-2-(7-(2-Amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-6-yl)heptanamido)pentanedioic acid
ChEMBLCHEMBL3086865
DrugBank
ZINCZINC000103278182
PDB chain4zyz Chain A Residue 1102 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4zyz Structural and Enzymatic Analysis of Tumor-Targeted Antifolates That Inhibit Glycinamide Ribonucleotide Formyltransferase.
Resolution1.6 Å
Binding residue
(original residue number in PDB)		R871 L892 F895 M896 R897 I898 L899 V946 A947 E948 V950
Binding residue
(residue number reindexed from 1)		R64 L85 F88 M89 R90 I91 L92 V139 A140 E141 V143
Annotation score1
Binding affinityMOAD: Ki=67nM
PDBbind-CN: -logKd/Ki=7.17,Ki=67nM
BindingDB: IC50=2.9nM
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

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Molecular Function
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Biological Process
External links
PDB RCSB:4zyz, PDBe:4zyz, PDBj:4zyz
PDBsum4zyz
PubMed27439469
UniProtP22102|PUR2_HUMAN Trifunctional purine biosynthetic protein adenosine-3 (Gene Name=GART)

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