Structure of PDB 3afo Chain B Binding Site BS01

Receptor Information
>3afo Chain B (length=341) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VKIKPVNNLRSSSSADFVSPPNSKLQSLIWQNPLQNVYITKKPWTPSTRE
AMVEFITHLHESYPEVNVIVQPDVAEEISQDFKSPLENDPNRPHILYTGP
EQDIVNRTDLLVTLGGDGTILHGVSMFGNTQVPPVLAFALGTLGFLSPFD
FKEHKKVFQEVISSRAKCLHRTRLECHLKKKDSNSSIVTHAMNDIFLHRG
NSPHLTNLDIFIDGEFLTRTTADGVALATPTGSTAYSLSAGGSIVSPLVP
AILMTPICPRSLSFRPLILPHSSHIRIKIGSSVVKLSVDGIPQQDLDVGD
EIYVINEVKRSGIYCVAKTENDWIRGINELLGFNSSFRLTK
Ligand information
Ligand IDNAI
InChIInChI=1S/C21H29N7O14P2/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(32)14(30)11(41-21)6-39-44(36,37)42-43(34,35)38-5-10-13(29)15(31)20(40-10)27-3-1-2-9(4-27)18(23)33/h1,3-4,7-8,10-11,13-16,20-21,29-32H,2,5-6H2,(H2,23,33)(H,34,35)(H,36,37)(H2,22,24,25)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKeyBOPGDPNILDQYTO-NNYOXOHSSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)N5C=CCC(=C5)C(=O)N)O)O)O)O)N
CACTVS 3.341NC(=O)C1=CN(C=CC1)[C@@H]2O[C@H](CO[P@@](O)(=O)O[P@](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)N5C=CCC(=C5)C(=O)N)O)O)O)O)N
CACTVS 3.341NC(=O)C1=CN(C=CC1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
FormulaC21 H29 N7 O14 P2
Name1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE;
NADH
ChEMBLCHEMBL1234616
DrugBankDB00157
ZINCZINC000008215403
PDB chain3afo Chain B Residue 1001 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3afo The structural factor conferring NADH kinase activity on yeast mitochondrial Pos5
Resolution2.0 Å
Binding residue
(original residue number in PDB)		D150 G151 L154 F178 N226 D227 T267 A268 Y269 S272 D330 G331
Binding residue
(residue number reindexed from 1)		D117 G118 L121 F145 N193 D194 T234 A235 Y236 S239 D289 G290
Annotation score4
Enzymatic activity
Enzyme Commision number 2.7.1.86: NADH kinase.
Gene Ontology
Molecular Function
GO:0003951 NAD+ kinase activity
GO:0005524 ATP binding
GO:0016301 kinase activity
GO:0016773 phosphotransferase activity, alcohol group as acceptor
GO:0042736 NADH kinase activity
Biological Process
GO:0006741 NADP biosynthetic process
GO:0016226 iron-sulfur cluster assembly
GO:0016310 phosphorylation
GO:0019674 NAD metabolic process
GO:0034599 cellular response to oxidative stress
Cellular Component
GO:0005739 mitochondrion
GO:0005759 mitochondrial matrix

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3afo, PDBe:3afo, PDBj:3afo
PDBsum3afo
PubMed
UniProtQ06892|POS5_YEAST NADH kinase POS5, mitochondrial (Gene Name=POS5)

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