Structure of PDB 3n34 Chain B Binding Site BS02

Receptor Information

>3n34 Chain B (length=322) Species: 36329 (Plasmodium falciparum 3D7)

SMGFKVKLEKRRNAINTCLCIGLDPDEKDIENFMKNEKENNYNNIKKNLK
EKYINNVSIKKDILLKAPDNIIREEKSEEFFYFFNHFCFYIINETNKYAL
TFKMNFAFYIPYGSVGIDVLKNVFDYLYELNIPTILDMKINDIGNTVKNY
RKFIFEYLKSDSCTVNIYMGTNMLKDICYDEEKNKYYSAFVLVKTTNPDS
AIFQKNLSLDNKQAYVIMAQEALNMSSYLNLEQNNEFIGFVVGANSYDEM
NYIRTYFPNCYILSPGIGAQNGDLHKTLTNGYHKSYEKILINIGRAITKN
PYPQKAAQMYYDQINAILKQNM

Ligand information

• Ligand ID: FNU
• InChI: InChI=1S/C9H13FN3O9P/c10-3-6(11)13(9(17)12-7(3)16)8-5(15)4(14)2(22-8)1-21-23(18,19)20/h2,4-5,8,14-15H,1,11H2,(H,12,16,17)(H2,18,19,20)/t2-,4-,5-,8-/m1/s1
• InChIKey: OLBMCLUPWOAIRA-UMMCILCDSA-N
• SMILES:
  ACDLabs 12.01: O=P(O)(O)OCC2OC(N1C(=O)NC(=O)C(F)=C1N)C(O)C2O
  CACTVS 3.370: NC1=C(F)C(=O)NC(=O)N1[CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O
  CACTVS 3.370: NC1=C(F)C(=O)NC(=O)N1[C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O
  OpenEye OEToolkits 1.7.0: C(C1C(C(C(O1)N2C(=C(C(=O)NC2=O)F)N)O)O)OP(=O)(O)O
  OpenEye OEToolkits 1.7.0: C([C@@H]1[C@H]([C@H]([C@@H](O1)N2C(=C(C(=O)NC2=O)F)N)O)O)OP(=O)(O)O
• Formula: C9 H13 F N3 O9 P
• Name: 6-amino-5-fluorouridine 5'-(dihydrogen phosphate)
• ChEMBL: CHEMBL474165
• ZINC: ZINC000040406933
• PDB chain: 3n34 Chain B Residue 1001

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3n34 Crystal structure of Plasmodium falciparum orotidine 5'-monophosphate decarboxylase complexed with 5-fluoro-6-amino-UMP, produced from 5-fluoro-6-azido-UMP
• Resolution: 1.55 Å
• Binding residue (original residue number in PDB): D23 K102 N104 D136 K138 T194 T195 P264 Q269 G293 R294
• Binding residue (residue number reindexed from 1): D24 K103 N105 D137 K139 T195 T196 P265 Q270 G294 R295
• Annotation score: 2

Enzymatic activity

• Enzyme Commision number: 4.1.1.23: orotidine-5'-phosphate decarboxylase.

Gene Ontology

Molecular Function

• GO:0004590 orotidine-5'-phosphate decarboxylase activity
• GO:0005515 protein binding
• GO:0016831 carboxy-lyase activity

Biological Process

• GO:0006207 'de novo' pyrimidine nucleobase biosynthetic process
• GO:0006221 pyrimidine nucleotide biosynthetic process
• GO:0044205 'de novo' UMP biosynthetic process

External links

• PDB: RCSB:3n34, PDBe:3n34, PDBj:3n34
• PDBsum: 3n34
• UniProt: Q8IJH3