Structure of PDB 4nfl Chain A Binding Site BS02

Receptor Information
>4nfl Chain A (length=201) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SNAASGGRALRVLVDMDGVLADFEGGFLRKFRARFPDQPFIALEDRRGFW
VSEQYGRLRPGLSEKAISIWESKNFFFELEPLPGAVEAVKEMASLQNTDV
FICTSPIKMFKYCPYEKYAWVEKYFGPDFLEQIVLTRDKTVVSADLLIDD
RPDITGAEPTPSWEHVLFTACHNQHLQLQPPRRRLHSWADDWKAILDSKR
P
Ligand information
Ligand ID2JW
InChIInChI=1S/C17H18N3O10P/c1-9-7-19(16(22)18-15(9)21)14-6-12-13(29-14)8-28-17(30-12,31(25,26)27)10-2-4-11(5-3-10)20(23)24/h2-5,7,12-14H,6,8H2,1H3,(H,18,21,22)(H2,25,26,27)/t12-,13-,14-,17-/m1/s1
InChIKeyBODNGCHFOUEZME-VMUDFCTBSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CC1=CN([CH]2C[CH]3O[C](OC[CH]3O2)(c4ccc(cc4)[N+]([O-])=O)[P](O)(O)=O)C(=O)NC1=O
OpenEye OEToolkits 1.7.6CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]3[C@H](O2)CO[C@@](O3)(c4ccc(cc4)[N+](=O)[O-])P(=O)(O)O
ACDLabs 12.01[O-][N+](=O)c1ccc(cc1)C3(OCC4OC(N2C=C(C(=O)NC2=O)C)CC4O3)P(=O)(O)O
OpenEye OEToolkits 1.7.6CC1=CN(C(=O)NC1=O)C2CC3C(O2)COC(O3)(c4ccc(cc4)[N+](=O)[O-])P(=O)(O)O
CACTVS 3.385CC1=CN([C@H]2C[C@H]3O[C@](OC[C@H]3O2)(c4ccc(cc4)[N+]([O-])=O)[P](O)(O)=O)C(=O)NC1=O
FormulaC17 H18 N3 O10 P
Name1-{2-deoxy-3,5-O-[(4-nitrophenyl)(phosphono)methylidene]-beta-D-threo-pentofuranosyl}-5-methylpyrimidine-2,4(1H,3H)-dione
ChEMBL
DrugBank
ZINCZINC000098208185
PDB chain4nfl Chain A Residue 303 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB4nfl Conformationally constrained nucleoside phosphonic acids - potent inhibitors of human mitochondrial and cytosolic 5'(3')-nucleotidases.
Resolution1.375 Å
Binding residue
(original residue number in PDB)		F75 W76 V77 W96 S131 I133 K134 R163
Binding residue
(residue number reindexed from 1)		F49 W50 V51 W70 S105 I107 K108 R137
Annotation score1
Binding affinityMOAD: Ki=22.1uM
Enzymatic activity
Catalytic site (original residue number in PDB) D41 D43 D176
Catalytic site (residue number reindexed from 1) D15 D17 D150
Enzyme Commision number 3.1.3.-
Gene Ontology
Molecular Function
GO:0008253 5'-nucleotidase activity
Biological Process
GO:0009264 deoxyribonucleotide catabolic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:4nfl, PDBe:4nfl, PDBj:4nfl
PDBsum4nfl
PubMed25178098
UniProtQ9NPB1|NT5M_HUMAN 5'(3')-deoxyribonucleotidase, mitochondrial (Gene Name=NT5M)

[Back to BioLiP]