Structure of PDB 2mas Chain A Binding Site BS02

Receptor Information

>2mas Chain A (length=313) Species: 5656 (Crithidia fasciculata)

AKKIILDCDPGLDDAVAILLAHGNPEIELLAITTVVGNQTLAKVTRNAQL
VADIAGITGVPIAAGCDKPLVRKIMTAGHIHGESGMGTVAYPAEFKNKVD
ERHAVNLIIDLVMSHEPKTITLVPTGGLTNIAMAARLEPRIVDRVKEVVL
MGGGYHEGNATSVAEFNIIIDPEAAHIVFNESWQVTMVGLDLTHQALATP
PILQRVKEVDTNPARFMLEIMDYYTKIYQSNRYMAAAAVHDPCAVAYVID
PSVMTTERVPVDIELTGKLTLGMTVADFRNPRPEHCHTQVAVKLDFEKFW
GLVLDALERIGDP

Ligand information

• Ligand ID: PIR
• InChI: InChI=1S/C11H16N2O3/c12-7-3-1-6(2-4-7)9-11(16)10(15)8(5-14)13-9/h1-4,8-11,13-16H,5,12H2/t8-,9+,10-,11+/m1/s1
• InChIKey: SQENVZNKXLCDLF-YTWAJWBKSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: c1cc(ccc1C2C(C(C(N2)CO)O)O)N
  OpenEye OEToolkits 1.5.0: c1cc(ccc1[C@H]2[C@@H]([C@@H]([C@H](N2)CO)O)O)N
  CACTVS 3.341: Nc1ccc(cc1)[C@@H]2N[C@H](CO)[C@@H](O)[C@H]2O
  CACTVS 3.341: Nc1ccc(cc1)[CH]2N[CH](CO)[CH](O)[CH]2O
  ACDLabs 10.04: OC2C(c1ccc(N)cc1)NC(CO)C2O
• Formula: C11 H16 N2 O3
• Name: 2-(4-AMINO-PHENYL)-5-HYDROXYMETHYL-PYRROLIDINE-3,4-DIOL
• ZINC: ZINC000005933433
• PDB chain: 2mas Chain A Residue 400

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2mas Trypanosomal nucleoside hydrolase. A novel mechanism from the structure with a transition-state inhibitor.
• Resolution: 2.3 Å
• Binding residue (original residue number in PDB): D14 N39 I81 M152 E166 F167 N168 D242
• Binding residue (residue number reindexed from 1): D13 N38 I80 M151 E165 F166 N167 D241
• Annotation score: 1
• Binding affinity: MOAD: Kd=30nM
  PDBbind-CN: -logKd/Ki=7.52,Kd=30nM

Enzymatic activity

• Catalytic site (original residue number in PDB): D10 D15 N39 I75 T126 F167 N168 H241 D242
• Catalytic site (residue number reindexed from 1): D9 D14 N38 I74 T125 F166 N167 H240 D241
• Enzyme Commision number: 3.2.2.2: inosine nucleosidase.
  3.2.2.3: uridine nucleosidase.

Gene Ontology

Molecular Function

• GO:0008477 purine nucleosidase activity
• GO:0016798 hydrolase activity, acting on glycosyl bonds
• GO:0016799 hydrolase activity, hydrolyzing N-glycosyl compounds
• GO:0045437 uridine nucleosidase activity
• GO:0046872 metal ion binding
• GO:0047724 inosine nucleosidase activity

Biological Process

• GO:0006139 nucleobase-containing compound metabolic process
• GO:0006152 purine nucleoside catabolic process
• GO:0009117 nucleotide metabolic process

Cellular Component

• GO:0005829 cytosol

External links

• PDB: RCSB:2mas, PDBe:2mas, PDBj:2mas
• PDBsum: 2mas
• PubMed: 9572842
• UniProt: Q27546|IUNH_CRIFA Inosine-uridine preferring nucleoside hydrolase (Gene Name=IUNH)