Structure of PDB 3uq8 Chain A Binding Site BS01

Receptor Information
>3uq8 Chain A (length=322) Species: 71421 (Haemophilus influenzae Rd KW20) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NIQTQLDNLRKTLRQYEYEYHVLDNPSVPDSEYDRLFHQLKALELEHPEF
LTSDSPTQRVGAKPLSGFSQIRHEIPMLSLDNAFSDAEFNAFVARIEDRL
ILLPAPLTFCCEPKLDGLAVSILYVNGELTQAATRGDGTTGEDITANIRT
IRNVPLQLLTDNPPARLEVRGEVFMPHAGFERLNKYALEHNEKTFANPRN
AAAGSLRQLDPNITSKRPLVLNAYGIGIAEGVDLPTTHYARLQWLKSIGI
PVNPEIRLCNGADEVLGFYRDIQNKRSSLGYDIDGTVLKINDIALQNELG
FISKAPRWAIAYKFPAQEELTL
Ligand information
Ligand IDNAD
InChIInChI=1S/C21H27N7O14P2/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/h1-4,7-8,10-11,13-16,20-21,29-32H,5-6H2,(H5-,22,23,24,25,33,34,35,36,37)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKeyBAWFJGJZGIEFAR-NNYOXOHSSA-N
SMILES
SoftwareSMILES
CACTVS 3.341NC(=O)c1ccc[n+](c1)[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 1.5.0c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)N
CACTVS 3.341NC(=O)c1ccc[n+](c1)[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
OpenEye OEToolkits 1.5.0c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)([O-])O[P@@](=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)N
FormulaC21 H27 N7 O14 P2
NameNICOTINAMIDE-ADENINE-DINUCLEOTIDE
ChEMBLCHEMBL1234613
DrugBankDB14128
ZINC
PDB chain3uq8 Chain A Residue 1 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB3uq8 Structure Guided Understanding of NAD(+) Recognition in Bacterial DNA Ligases.
Resolution1.7 Å
Binding residue
(original residue number in PDB)		Y18 Y22 D32 Y35 D36 F39 H40 K43 R154
Binding residue
(residue number reindexed from 1)		Y16 Y20 D30 Y33 D34 F37 H38 K41 R152
Annotation score4
Binding affinityMOAD: Kd=45uM
Enzymatic activity
Catalytic site (original residue number in PDB) E114 K116 D118 Y226 K315
Catalytic site (residue number reindexed from 1) E112 K114 D116 Y224 K313
Enzyme Commision number 6.5.1.2: DNA ligase (NAD(+)).
Gene Ontology
Molecular Function
GO:0003911 DNA ligase (NAD+) activity

View graph for
Molecular Function
External links
PDB RCSB:3uq8, PDBe:3uq8, PDBj:3uq8
PDBsum3uq8
PubMed22230472
UniProtP43813|DNLJ_HAEIN DNA ligase (Gene Name=ligA)

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