Structure of PDB 3gf4 Chain A Binding Site BS02

Receptor Information

>3gf4 Chain A (length=383) Species: 573 (Klebsiella pneumoniae)

KSKKILIVGAGFSGAVIGRQLAEKGHQVHIIDQRDHIGGNSYDARDSETN
VMVHVYGPHIFHTDNETVWNYINKHAEMMPYVNRVKATVNGQVFSLPINL
HTINQFFSKTCSPDEARALIAEKGDSTIADPQTFEEQALRFIGKELYEAF
FKGYTIKQWGMQPSELPASILKRLPVRFNYDDNYFNHKFQGMPKCGYTQM
IKSILNHENIKVDLQREFIVDERTHYDHVFYSGPLDAFYGYQYGRLGYRT
LDFKKFIYQGDYQGCAVMNYCSVDVPYTRITEHKYFSPWEQHDGSVCYKE
YSRACEENDIPYYPIRQMGEMALLEKYLSLAENETNITFVGRLGTYRYLD
MDVTIAEALKTAEVYLNSLTDNQPMPVFTVSVG

Ligand information

• Ligand ID: UPG
• InChI: InChI=1S/C15H24N2O17P2/c18-3-5-8(20)10(22)12(24)14(32-5)33-36(28,29)34-35(26,27)30-4-6-9(21)11(23)13(31-6)17-2-1-7(19)16-15(17)25/h1-2,5-6,8-14,18,20-24H,3-4H2,(H,26,27)(H,28,29)(H,16,19,25)/t5-,6-,8-,9-,10+,11-,12-,13-,14-/m1/s1
• InChIKey: HSCJRCZFDFQWRP-JZMIEXBBSA-N
• SMILES:
  CACTVS 3.370: OC[C@H]1O[C@H](O[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@H](O)[C@@H](O)[C@@H]1O
  ACDLabs 12.01: O=C1C=CN(C(=O)N1)C2OC(C(O)C2O)COP(=O)(OP(=O)(OC3OC(C(O)C(O)C3O)CO)O)O
  CACTVS 3.370: OC[CH]1O[CH](O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)N3C=CC(=O)NC3=O)[CH](O)[CH](O)[CH]1O
  OpenEye OEToolkits 1.7.6: C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@](=O)(O)O[P@](=O)(O)O[C@@H]3[C@@H]([C@H]([C@@H]([C@H](O3)CO)O)O)O)O)O
  OpenEye OEToolkits 1.7.6: C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OC3C(C(C(C(O3)CO)O)O)O)O)O
• Formula: C15 H24 N2 O17 P2
• Name: URIDINE-5'-DIPHOSPHATE-GLUCOSE;
  URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER
• ChEMBL: CHEMBL375951
• DrugBank: DB01861
• ZINC: ZINC000008215472
• PDB chain: 3gf4 Chain A Residue 392

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3gf4 Ligand binding and substrate discrimination by UDP-galactopyranose mutase.
• Resolution: 2.45 Å
• Binding residue (original residue number in PDB): F152 Y155 T156 Q159 W160 L175 Y185 N270 R280 Y314
• Binding residue (residue number reindexed from 1): F151 Y154 T155 Q158 W159 L174 Y184 N269 R279 Y313
• Annotation score: 4
• Binding affinity: MOAD: Kd=750uM

Enzymatic activity

• Catalytic site (original residue number in PDB): R174 R178 R250 R280 E301 Y349 D351
• Catalytic site (residue number reindexed from 1): R173 R177 R249 R279 E300 Y348 D350
• Enzyme Commision number: 5.4.99.9: UDP-galactopyranose mutase.

Gene Ontology

Molecular Function

• GO:0008767 UDP-galactopyranose mutase activity

External links

• PDB: RCSB:3gf4, PDBe:3gf4, PDBj:3gf4
• PDBsum: 3gf4
• PubMed: 19500588
• UniProt: Q48485|GLF1_KLEPN UDP-galactopyranose mutase (Gene Name=rfbD)