Structure of PDB 3pn1 Chain A Binding Site BS01

Receptor Information
>3pn1 Chain A (length=318) Species: 727 (Haemophilus influenzae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MTNIQTQLDNLRKTLRQYEYEYHVLDNPSVPDSEYDRLFHQLKALELEHP
EFLTSDSPTQRVGAKPLSGFSQIRHEIPMLSLDNAFSDAEFNAFVKRIED
RLILLPKPLTFCCEPKLDGLAVSILYVNGELTQAATRGDGTTGEDITANI
RTIRNVPLQLLTDNPPARLEVRGEVFMPHAGFERLNKYALEHNEKTFANP
RNAAAGSLRQLDPNITSKRPLVLNAYGIGIAEGVDLPTTHYARLQWLKSI
GIPVNPEIRLCNGADEVLGFYRDIQNKRSSLGYDIDGTVLKINDIALQNE
LGFISKAPRWAIAYKFPA
Ligand information
Ligand IDIVH
InChIInChI=1S/C14H21N5O4S/c1-2-3-4-24-14-17-11(15)8-12(18-14)19(6-16-8)13-10(22)9(21)7(5-20)23-13/h6-7,9-10,13,20-22H,2-5H2,1H3,(H2,15,17,18)/t7-,9-,10-,13-/m1/s1
InChIKeyJUZWTKSKLZRPBL-QYVSTXNMSA-N
SMILES
SoftwareSMILES
CACTVS 3.370CCCCSc1nc(N)c2ncn([CH]3O[CH](CO)[CH](O)[CH]3O)c2n1
OpenEye OEToolkits 1.7.0CCCCSc1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO)O)O)N
ACDLabs 12.01n2c1c(nc(SCCCC)nc1n(c2)C3OC(C(O)C3O)CO)N
OpenEye OEToolkits 1.7.0CCCCSc1nc(c2c(n1)n(cn2)C3C(C(C(O3)CO)O)O)N
CACTVS 3.370CCCCSc1nc(N)c2ncn([C@@H]3O[C@H](CO)[C@@H](O)[C@H]3O)c2n1
FormulaC14 H21 N5 O4 S
Name2-(butylsulfanyl)adenosine
ChEMBLCHEMBL1233689
DrugBank
ZINCZINC000039178283
PDB chain3pn1 Chain A Residue 319 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3pn1 Novel Bacterial NAD+-Dependent DNA Ligase Inhibitors with Broad-Spectrum Activity and Antibacterial Efficacy In Vivo.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		L82 E114 K116 L117 E174 Y226 V289 K291 P308
Binding residue
(residue number reindexed from 1)		L82 E114 K116 L117 E174 Y226 V289 K291 P308
Annotation score1
Binding affinityMOAD: Ki=110nM
PDBbind-CN: -logKd/Ki=6.96,Ki=110nM
Enzymatic activity
Catalytic site (original residue number in PDB) E114 K116 D118 Y226 K315
Catalytic site (residue number reindexed from 1) E114 K116 D118 Y226 K315
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:3pn1, PDBe:3pn1, PDBj:3pn1
PDBsum3pn1
PubMed21189350
UniProtP43813|DNLJ_HAEIN DNA ligase (Gene Name=ligA)

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