Structure of PDB 1mn7 Chain B Binding Site BS01

Receptor Information
>1mn7 Chain B (length=150) Species: 44689 (Dictyostelium discoideum) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VNKERTFLAVKPDGVARGLVGEIIARYEKKGFVLVGLKQLVPTKDLAESH
YAEHKERPWFGGLVSFITSGPVVAMVFEGKGVVASARLMIGVTNPLASAP
GSIRGDFGVDVGRSIIGGSDSVESANREIALWFKPEELLTEVKPNPNLYE
Ligand information
Ligand IDABT
InChIInChI=1S/C10H17BN5O12P3/c1-5-3-16(10(18)13-9(5)17)8-2-6(14-15-12)7(26-8)4-25-29(11,19)27-31(23,24)28-30(20,21)22/h3,6-8,11,19H,2,4H2,1H3,(H,23,24)(H,13,17,18)(H2,20,21,22)/t6-,7+,8+,29+/m0/s1
InChIKeyYRFDNFJEDDBNDW-NYNRLPRQSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CC1=CN([C@H]2C[C@H](N=[N+]=[N-])[C@@H](CO[P@](O)(=B)O[P](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O
OpenEye OEToolkits 1.7.5B=P(O)(OC[C@@H]1[C@H](C[C@@H](O1)N2C=C(C(=O)NC2=O)C)N=[N+]=[N-])O[P@](=O)(O)OP(=O)(O)O
CACTVS 3.385CC1=CN([CH]2C[CH](N=[N+]=[N-])[CH](CO[P](O)(=B)O[P](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=B)(O)OCC2OC(N1C(=O)NC(=O)C(=C1)C)CC2\N=[N+]=[N-]
OpenEye OEToolkits 1.7.5B=P(O)(OCC1C(CC(O1)N2C=C(C(=O)NC2=O)C)N=[N+]=[N-])OP(=O)(O)OP(=O)(O)O
FormulaC10 H17 B N5 O12 P3
Name3'-AZIDO-3'-DEOXY-THYMIDINE-5'-ALPHA BORANO TRIPHOSPHATE
ChEMBL
DrugBank
ZINCZINC000263621298
PDB chain1mn7 Chain B Residue 2160 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1mn7 Improving nucleoside diphosphate kinase for antiviral nucleotide analogs activation
Resolution2.15 Å
Binding residue
(original residue number in PDB)		Y56 H59 W64 L68 R92 R109 S119 G122 G123
Binding residue
(residue number reindexed from 1)		Y51 H54 W59 L63 R87 R104 S114 G117 G118
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) K16 Y56 S119 G122 E133
Catalytic site (residue number reindexed from 1) K11 Y51 S114 G117 E128
Enzyme Commision number 2.7.4.6: nucleoside-diphosphate kinase.
Gene Ontology
Molecular Function
GO:0004550 nucleoside diphosphate kinase activity
GO:0005524 ATP binding
GO:0016301 kinase activity
GO:0046872 metal ion binding
Biological Process
GO:0006183 GTP biosynthetic process
GO:0006187 dGTP biosynthetic process from dGDP
GO:0006228 UTP biosynthetic process
GO:0006241 CTP biosynthetic process
GO:0006414 translational elongation
GO:0007186 G protein-coupled receptor signaling pathway
GO:0009117 nucleotide metabolic process
GO:0009142 nucleoside triphosphate biosynthetic process
GO:0009617 response to bacterium
GO:0016310 phosphorylation
GO:0019954 asexual reproduction
GO:0030036 actin cytoskeleton organization
GO:0045920 negative regulation of exocytosis
GO:0048550 negative regulation of pinocytosis
GO:0050765 negative regulation of phagocytosis
Cellular Component
GO:0005737 cytoplasm
GO:0005840 ribosome
GO:0005856 cytoskeleton
GO:0005886 plasma membrane
GO:0015629 actin cytoskeleton
GO:0030141 secretory granule
GO:0045335 phagocytic vesicle

View graph for
Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:1mn7, PDBe:1mn7, PDBj:1mn7
PDBsum1mn7
PubMed12171931
UniProtP22887|NDKC_DICDI Nucleoside diphosphate kinase, cytosolic (Gene Name=ndkC-1)

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