Structure of PDB 3sxp Chain D Binding Site BS01

Receptor Information

>3sxp Chain D (length=314) Species: 563041 (Helicobacter pylori G27)

MRYIDDELENQTILITGGAGFVGSNLAFHFQENHPKAKVVVLDKFRSNPS
SLGHFKNLIGFKGEVIAADINNPLDLRRLEKLHFDYLFHQAAVSDTTMLN
QELVMKTNYQAFLNLLEIARSKKAKVIYASSAGVYGNTKAPNVVGKNESP
ENVYGFSKLCMDEFVLSHSNDNVQVGLRYFNVYGPREFYKEKTASMVLQL
ALGAMAFKEVKLFEFGEQLRDFVYIEDVIQANVKAMKAQKSGVYNVGYSQ
ARSYNEIVSILKEHLGDFKVTYIKNFFQKHTQAHIEPTILDLDYTPLYDL
ESGIKDYLPHIHAI

Ligand information

• Ligand ID: NAD
• InChI: InChI=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
• InChIKey: BAWFJGJZGIEFAR-NNYOXOHSSA-N
• SMILES:
  CACTVS 3.341: NC(=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 1.5.0: c1cc(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 3.341: NC(=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 1.5.0: c1cc(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
• Formula: C21 H27 N7 O14 P2
• Name: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
• ChEMBL: CHEMBL1234613
• DrugBank: DB14128
• PDB chain: 3sxp Chain D Residue 2401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3sxp The crystal structure of ADP-L-glycero-D-manno-heptose-6-epimerase (HP0859) from Helicobacter pylori.
• Resolution: 2.55 Å
• Binding residue (original residue number in PDB): G17 G20 F21 V22 D43 K44 S58 G60 D76 I77 Q97 A98 A99 A136 S138 Y161 K165 Y186 N188 V189 K197
• Binding residue (residue number reindexed from 1): G17 G20 F21 V22 D43 K44 S51 G53 D69 I70 Q90 A91 A92 A129 S131 Y154 K158 Y179 N181 V182 K190
• Annotation score: 2

Enzymatic activity

• Catalytic site (original residue number in PDB): S138 A139 G140 Y161 F163 K165 K197
• Catalytic site (residue number reindexed from 1): S131 A132 G133 Y154 F156 K158 K190
• Enzyme Commision number: 5.1.3.20: ADP-glyceromanno-heptose 6-epimerase.

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0008712 ADP-glyceromanno-heptose 6-epimerase activity
• GO:0016853 isomerase activity
• GO:0050661 NADP binding

Biological Process

• GO:0005975 carbohydrate metabolic process

External links

• PDB: RCSB:3sxp, PDBe:3sxp, PDBj:3sxp
• PDBsum: 3sxp
• PubMed: 21979583
• UniProt: B5Z7L9