Structure of PDB 3ara Chain A Binding Site BS01

Receptor Information
>3ara Chain A (length=125) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MQLRFARLSEHATAPTRGSARAAGYDLYSAYDYTIPPMEKAVVKTDIQIA
LPSGCYGRVAPRSGLAAKHFIDVGAGVIDEDYRGNVGVVLFNFGKEKFEV
KKGDRIAQLICERIFYPEIEEVQAL
Ligand information
Ligand IDMKH
InChIInChI=1S/C24H27N3O5S/c28-22-14-17-26(23(29)25-22)15-8-18-33(31,32)27-16-7-13-21(27)24(30,19-9-3-1-4-10-19)20-11-5-2-6-12-20/h1-6,9-12,14,17,21,30H,7-8,13,15-16,18H2,(H,25,28,29)/t21-/m1/s1
InChIKeyNBGXNYZRJDHHHU-OAQYLSRUSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=S(=O)(N3C(C(O)(c1ccccc1)c2ccccc2)CCC3)CCCN4C=CC(=O)NC4=O
OpenEye OEToolkits 1.7.0c1ccc(cc1)C(c2ccccc2)([C@H]3CCCN3S(=O)(=O)CCCN4C=CC(=O)NC4=O)O
CACTVS 3.370OC([CH]1CCCN1[S](=O)(=O)CCCN2C=CC(=O)NC2=O)(c3ccccc3)c4ccccc4
OpenEye OEToolkits 1.7.0c1ccc(cc1)C(c2ccccc2)(C3CCCN3S(=O)(=O)CCCN4C=CC(=O)NC4=O)O
CACTVS 3.370OC([C@H]1CCCN1[S](=O)(=O)CCCN2C=CC(=O)NC2=O)(c3ccccc3)c4ccccc4
FormulaC24 H27 N3 O5 S
Name1-[3-({(2R)-2-[hydroxy(diphenyl)methyl]pyrrolidin-1-yl}sulfonyl)propyl]pyrimidine-2,4(1H,3H)-dione
ChEMBLCHEMBL1234349
DrugBank
ZINCZINC000058651014
PDB chain3ara Chain A Residue 165 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3ara Synthesis and discovery of N-carbonylpyrrolidine- or N-sulfonylpyrrolidine-containing uracil derivatives as potent human deoxyuridine triphosphatase inhibitors
Resolution1.7 Å
Binding residue
(original residue number in PDB)		V65 G99 V100 Y105 G110
Binding residue
(residue number reindexed from 1)		V42 G76 V77 Y82 G87
Annotation score1
Binding affinityMOAD: ic50=0.32uM
PDBbind-CN: -logKd/Ki=6.49,IC50=0.32uM
BindingDB: IC50=480nM
Enzymatic activity
Catalytic site (original residue number in PDB) A46 R85 G87 I94 D102
Catalytic site (residue number reindexed from 1) A23 R62 G64 I71 D79
Enzyme Commision number 3.6.1.23: dUTP diphosphatase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0004170 dUTP diphosphatase activity
Biological Process
GO:0006226 dUMP biosynthetic process
GO:0046081 dUTP catabolic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3ara, PDBe:3ara, PDBj:3ara
PDBsum3ara
PubMed22404301
UniProtP33316|DUT_HUMAN Deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial (Gene Name=DUT)

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