Structure of PDB 2y4m Chain A Binding Site BS02

Receptor Information

>2y4m Chain A (length=377) Species: 518766 (Rhodothermus marinus DSM 4252)

SLVVFPFKHEHPEVLLHNVRVAAAHPRVHEVLCIGYERDQTYEAVERAAP
EISRATGTPVSVRLQERLGTLRPGKGDGMNTALRYFLEETQWERIHFYDA
DITSFGPDWITKAEEAADFGYGLVRHYFPRASTDAMITWMITRTGFALLW
PHTELSWIEQPLGGELLMRREVAAMLYEDERVRRRSDWGIDTLYTFVTVA
AGVSIYECYIPEGKAHRLLDDLRTMLVECFAAIQSLQHEVVGQPAIHRQE
HPHRVPVHIAERVGYDVEATLHRLMQHWTPRQVELLELFTTPVREGLRTC
QRRPAFNFMDEMAWAATYHVLLEHFQPGDPDWEELLFKLWTTRVLNYTMT
VALRGYDYAQQYLYRMLGRYRYQAALE

Ligand information

• Ligand ID: GDX
• InChI: InChI=1S/C16H23N5O17P2/c17-16-19-11-4(12(27)20-16)18-2-21(11)13-8(25)5(22)3(35-13)1-34-39(30,31)38-40(32,33)37-15-9(26)6(23)7(24)10(36-15)14(28)29/h2-3,5-10,13,15,22-26H,1H2,(H,28,29)(H,30,31)(H,32,33)(H3,17,19,20,27)/t3-,5-,6+,7+,8-,9+,10+,13-,15-/m1/s1
• InChIKey: DNBSDUDYNPJVCN-ZXTXFPBHSA-N
• SMILES:
  CACTVS 3.370: NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[CH]4O[CH]([CH](O)[CH](O)[CH]4O)C(O)=O)[CH](O)[CH]3O
  CACTVS 3.370: NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[C@H]4O[C@@H]([C@@H](O)[C@H](O)[C@@H]4O)C(O)=O)[C@@H](O)[C@H]3O
  OpenEye OEToolkits 1.7.0: c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(O)O[C@@H]4[C@H]([C@H]([C@@H]([C@H](O4)C(=O)O)O)O)O)O)O)N=C(NC2=O)N
  OpenEye OEToolkits 1.7.0: c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OC4C(C(C(C(O4)C(=O)O)O)O)O)O)O)N=C(NC2=O)N
  ACDLabs 12.01: O=C4NC(=Nc1c4ncn1C2OC(C(O)C2O)COP(=O)(OP(=O)(OC3OC(C(=O)O)C(O)C(O)C3O)O)O)N
• Formula: C16 H23 N5 O17 P2
• Name: GUANOSINE 5'-(TRIHYDROGEN DIPHOSPHATE), P'-D-MANNOPYRANOSYL ESTER
• DrugBank: DB04023
• ZINC: ZINC000008216635
• PDB chain: 2y4m Chain A Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2y4m Substrate and Metal Ion Promiscuity in Mannosylglycerate Synthase.
• Resolution: 2.7 Å
• Binding residue (original residue number in PDB): P7 F8 K9 E11 I35 Q66 G75 K76 D100 A101 D102 L163 G165 W189 D192 H217
• Binding residue (residue number reindexed from 1): P6 F7 K8 E10 I34 Q65 G74 K75 D99 A100 D101 L162 G164 W188 D191 H216
• Annotation score: 3
• Binding affinity: PDBbind-CN: -logKd/Ki=6.46,Kd=0.345uM

Enzymatic activity

• Enzyme Commision number: 2.4.1.217: mannosyl-3-phosphoglycerate synthase.

Gene Ontology

Molecular Function

• GO:0046872 metal ion binding

External links

• PDB: RCSB:2y4m, PDBe:2y4m, PDBj:2y4m
• PDBsum: 2y4m
• PubMed: 21288903
• UniProt: D0MI02