Structure of PDB 1g9r Chain A Binding Site BS02

Receptor Information

>1g9r Chain A (length=278) Species: 487 (Neisseria meningitidis)

MDIVFAADDNYAAYLCVAAKSVEAAHPDTEIRFHVLDAGISEANRAAVAA
NLRGGGGNIRFIDVNPEDFAGFPLNIRHISITTYARLKLGEYIADCDKVL
YLDIDVLVRDSLTPLWDTDLGDNWLGASIDLFVERQEGYKQKIGMADGEY
YFNAGVLLINLKKWRRHDIFKMSSEWVEQYKDVMQYQDQDILNGLFKGGV
CYANSRFNFMPTNYAFMASRHTDPLYRDRTNTVMPVAVSHYCGPAKPWHR
DCTAWGAERFTELAGSLTTVPEEWRGKL

Ligand information

• Ligand ID: UPF
• InChI: InChI=1S/C15H23FN2O16P2/c16-8-11(23)9(21)5(3-19)32-14(8)33-36(28,29)34-35(26,27)30-4-6-10(22)12(24)13(31-6)18-2-1-7(20)17-15(18)25/h1-2,5-6,8-14,19,21-24H,3-4H2,(H,26,27)(H,28,29)(H,17,20,25)/t5-,6-,8-,9+,10-,11-,12-,13-,14-/m1/s1
• InChIKey: NGTCPFGWXMBZEP-KBQKSTHMSA-N
• SMILES:
  CACTVS 3.341: 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](F)[C@@H](O)[C@H]1O
  ACDLabs 10.04: O=P(OC1OC(C(O)C(O)C1F)CO)(O)OP(=O)(O)OCC3OC(N2C=CC(=O)NC2=O)C(O)C3O
  OpenEye OEToolkits 1.5.0: C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OC3C(C(C(C(O3)CO)O)O)F)O)O
  OpenEye OEToolkits 1.5.0: 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)F)O)O
  CACTVS 3.341: 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](F)[CH](O)[CH]1O
• Formula: C15 H23 F N2 O16 P2
• Name: URIDINE-5'-DIPHOSPHATE-2-DEOXY-2-FLUOROGALACTOSE;
  URIDINE-5'-MONOPHOSPHATE 2-DEOXY-2-FLUORO-GALACTOPYRANOSYL-MONOPHOSPHATE ESTER
• DrugBank: DB02976
• ZINC: ZINC000015553713
• PDB chain: 1g9r Chain A Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1g9r Crystal structure of the retaining galactosyltransferase LgtC from Neisseria meningitidis in complex with donor and acceptor sugar analogs.
• Resolution: 2.0 Å
• Binding residue (original residue number in PDB): A6 A7 D8 Y11 H78 I79 S80 T83 R86 D103 I104 D105 N153 A154 Q187 D188 Q189 H244 C246 G247 K250
• Binding residue (residue number reindexed from 1): A6 A7 D8 Y11 H78 I79 S80 T83 R86 D103 I104 D105 N153 A154 Q187 D188 Q189 H240 C242 G243 K246
• Annotation score: 1
• Binding affinity: MOAD: Ki=2uM
  PDBbind-CN: -logKd/Ki=5.70,Ki=2uM

Enzymatic activity

• Catalytic site (original residue number in PDB): H78 D103 D105 D130 D188 Q189 H244 K250
• Catalytic site (residue number reindexed from 1): H78 D103 D105 D130 D188 Q189 H240 K246
• Enzyme Commision number: 2.4.1.-

Gene Ontology

Molecular Function

• GO:0016740 transferase activity
• GO:0016757 glycosyltransferase activity
• GO:0046872 metal ion binding

External links

• PDB: RCSB:1g9r, PDBe:1g9r, PDBj:1g9r
• PDBsum: 1g9r
• PubMed: 11175908
• UniProt: Q93EK7