Structure of PDB 4o9k Chain B Binding Site BS01

Receptor Information

>4o9k Chain B (length=128) Species: 243233 (Methylococcus capsulatus str. Bath)

RLLTFVRDIMHTGDDTPVIGLEASVRDALLEMTAKKLGMTAIVDGAGTIQ
GVFTDGDLRRLLEKAQDIHATPITAVMTRSCVTVEGSLLAAEAVRIMEQK
RINALPVVENGRLIGAINMHDLLRAGVL

Ligand information

• Ligand ID: CMK
• InChI: InChI=1S/C17H26N3O15P/c18-9-1-2-20(16(29)19-9)14-12(26)11(25)8(33-14)5-32-36(30,31)35-17(15(27)28)3-6(22)10(24)13(34-17)7(23)4-21/h1-2,6-8,10-14,21-26H,3-5H2,(H,27,28)(H,30,31)(H2,18,19,29)/t6-,7-,8-,10-,11-,12-,13-,14-,17-/m1/s1
• InChIKey: YWWJKULNWGRYAS-UOVSKDHASA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: C1[C@H]([C@H]([C@H](O[C@@]1(C(=O)O)O[P@@](=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)N3C=CC(=NC3=O)N)O)O)[C@@H](CO)O)O)O
  CACTVS 3.341: NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P@@](O)(=O)O[C@]3(C[C@@H](O)[C@@H](O)[C@H](O3)[C@H](O)CO)C(O)=O)[C@@H](O)[C@H]2O
  CACTVS 3.341: NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(=O)O[C]3(C[CH](O)[CH](O)[CH](O3)[CH](O)CO)C(O)=O)[CH](O)[CH]2O
  ACDLabs 10.04: O=C(O)C1(OC(C(O)CO)C(O)C(O)C1)OP(=O)(O)OCC3OC(N2C(=O)N=C(N)C=C2)C(O)C3O
  OpenEye OEToolkits 1.5.0: C1C(C(C(OC1(C(=O)O)OP(=O)(O)OCC2C(C(C(O2)N3C=CC(=NC3=O)N)O)O)C(CO)O)O)O
• Formula: C17 H26 N3 O15 P
• Name: CYTIDINE 5'-MONOPHOSPHATE 3-DEOXY-BETA-D-GULO-OCT-2-ULO-PYRANOSONIC ACID;
  CMP-2-KETO-3-DEOXY-OCTULOSONIC ACID
• DrugBank: DB04482
• ZINC: ZINC000030725157
• PDB chain: 4o9k Chain A Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4o9k Crystal structure and kinetic properties of D-arabinose 5-phosphate isomerase from Methylococcus capsulatus
• Resolution: 1.85 Å
• Binding residue (original residue number in PDB): K239 G241 D258 N321 H323
• Binding residue (residue number reindexed from 1): K36 G38 D55 N118 H120
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 5.3.1.13: arabinose-5-phosphate isomerase.

External links

• PDB: RCSB:4o9k, PDBe:4o9k, PDBj:4o9k
• PDBsum: 4o9k
• UniProt: Q60AU8