Structure of PDB 3q2k Chain M Binding Site BS02

Receptor Information

>3q2k Chain M (length=346) Species: 257313 (Bordetella pertussis Tohama I)

PITDRKIRFGLVGCGRISKNHIGAIAQHGDRAELVEICDTNPEALQAAEA
ATGARPFSSLSDMLAQGNADALVLATPSGLHPWQAIEVAQAGRHVVSEKP
MATRWEDGKRMVKACDEAGVRLFVVKQNRRNATLQLVKKAIEQGRFGRIY
MVTVNVFWTRPQEYYDAARWRGKWEWDGGAFMNQASHYVDLLDWLVGPVE
SVYAYTATLARRIEAEDTGVAALRWRHGAMGSINVTMLTYPQNLEGSITI
LGEKGTVRVGGVAVNRIDEWKFAEPHPDDDKIREANYETTSVYGFGHPLY
YDNVINCLRGDCEPETDGREGLQSLALLTAIYRSARDGVRIPLPLD

Ligand information

• Ligand ID: HP7
• InChI: InChI=1S/C17H25N3O18P2/c1-5(21)18-8-10(24)11(25)13(15(27)28)36-16(8)37-40(32,33)38-39(30,31)34-4-6-9(23)12(26)14(35-6)20-3-2-7(22)19-17(20)29/h2-3,6,8-14,16,23-26H,4H2,1H3,(H,18,21)(H,27,28)(H,30,31)(H,32,33)(H,19,22,29)/t6-,8-,9-,10-,11+,12-,13+,14-,16-/m1/s1
• InChIKey: DZOGQXKQLXAPND-HHKCBAECSA-N
• SMILES:
  OpenEye OEToolkits 1.7.0: CC(=O)N[C@@H]1[C@H]([C@@H]([C@H](O[C@@H]1O[P@@](=O)(O)O[P@@](=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)N3C=CC(=O)NC3=O)O)O)C(=O)O)O)O
  CACTVS 3.370: CC(=O)N[C@@H]1[C@@H](O)[C@H](O)[C@H](O[C@@H]1O[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)N3C=CC(=O)NC3=O)C(O)=O
  OpenEye OEToolkits 1.7.0: CC(=O)NC1C(C(C(OC1OP(=O)(O)OP(=O)(O)OCC2C(C(C(O2)N3C=CC(=O)NC3=O)O)O)C(=O)O)O)O
  ACDLabs 12.01: O=C1C=CN(C(=O)N1)C2OC(C(O)C2O)COP(=O)(OP(=O)(OC3OC(C(=O)O)C(O)C(O)C3NC(=O)C)O)O
  CACTVS 3.370: CC(=O)N[CH]1[CH](O)[CH](O)[CH](O[CH]1O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)N3C=CC(=O)NC3=O)C(O)=O
• Formula: C17 H25 N3 O18 P2
• Name: (2S,3S,4R,5R,6R)-5-acetamido-6-[[[(2R,3S,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy-hydroxy-phosphoryl]oxy-3,4-dihydroxy-oxane-2-carboxylic acid
• ZINC: ZINC000024617040
• PDB chain: 3q2k Chain M Residue 550

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3q2k Biochemical and Structural Characterization of WlbA from Bordetella pertussis and Chromobacterium violaceum: Enzymes Required for the Biosynthesis of 2,3-Diacetamido-2,3-dideoxy-d-mannuronic Acid.
• Resolution: 2.13 Å
• Binding residue (original residue number in PDB): R20 K103 T163 R164 Y168 N187 Q188 H191 Q246 N247
• Binding residue (residue number reindexed from 1): R16 K99 T159 R160 Y164 N183 Q184 H187 Q242 N243
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): K103 H191
• Catalytic site (residue number reindexed from 1): K99 H187

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding

External links

• PDB: RCSB:3q2k, PDBe:3q2k, PDBj:3q2k
• PDBsum: 3q2k
• PubMed: 21241053
• UniProt: Q79H45