Structure of PDB 1rkx Chain A Binding Site BS01

Receptor Information

>1rkx Chain A (length=349) Species: 633 (Yersinia pseudotuberculosis)

INNSFWQGKRVFVTGHTGFKGGWLSLWLQTMGATVKGYSLTAPTVPSLFE
TARVADGMQSEIGDIRDQNKLLESIREFQPEIVFHMAAQPLVRLSYSEPV
ETYSTNVMGTVYLLEAIRHVGGVKAVVNITSDKCYDNKEWIWGYRENEAM
GGYDPYSNSKGCAELVTSSYRNSFFNPANYGQHGTAVATVRAGNVIGGGD
WALDRIVPDILRAFEQSQPVIIRNPHAIRPWQHVLEPLSGYLLLAQKLYT
DGAEYAEGWNFGPNDADATPVKNIVEQMVKYWGEGASWQLEAHYLKLDCS
KAKMQLGWHPRWNLNTTLEYIVGWHKNWLSGTDMHEYSITEINNYMNTK

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: 1rkx Chain A Residue 360

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1rkx Crystal Structure at 1.8 A Resolution of CDP-d-Glucose 4,6-Dehydratase from Yersinia pseudotuberculosis
• Resolution: 1.8 Å
• Binding residue (original residue number in PDB): G16 T18 G19 F20 K21 S40 L41 D65 I66 M87 A88 A89 P91 T106 I130 S132 Y157 K161 A193 V196
• Binding residue (residue number reindexed from 1): G15 T17 G18 F19 K20 S39 L40 D64 I65 M86 A87 A88 P90 T105 I129 S131 Y156 K160 A192 V195
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): T131 S132 D133 K134 Y157 K161
• Catalytic site (residue number reindexed from 1): T130 S131 D132 K133 Y156 K160
• Enzyme Commision number: 4.2.1.45: CDP-glucose 4,6-dehydratase.

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0016829 lyase activity
• GO:0047733 CDP-glucose 4,6-dehydratase activity

External links

• PDB: RCSB:1rkx, PDBe:1rkx, PDBj:1rkx
• PDBsum: 1rkx
• PubMed: 15023057
• UniProt: Q57329