Structure of PDB 3bmq Chain A Binding Site BS02

Receptor Information

>3bmq Chain A (length=253) Species: 5702 (Trypanosoma brucei brucei)

EAPAAVVTGAAKRIGRAIAVKLHQTGYRVVIHYHNSAEAAVSLADELNKE
RSNTAVVCQADLTNSNVLPASCEEIINSCFRAFGRCDVLVNNASAFYPTP
LVQGKTVETQVAELIGTNAIAPFLLTMSFAQRQKGSSNLSIVNLCDAMVD
QPCMAFSLYNMGKHALVGLTQSAALELAPYGIRVNGVAPGVSLLPVAMGE
EEKDKWRRKVPLGRREASAEQIADAVIFLVSGSAQYITGSIIKVDGGLSL
VHA

Ligand information

• Ligand ID: AX5
• InChI: InChI=1S/C11H12N4S/c12-9-6-10(15-11(13)14-9)16-7-8-4-2-1-3-5-8/h1-6H,7H2,(H4,12,13,14,15)
• InChIKey: ATPMWVFWJFZLJM-UHFFFAOYSA-N
• SMILES:
  ACDLabs 10.04: S(c1nc(nc(N)c1)N)Cc2ccccc2
  CACTVS 3.341: Nc1cc(SCc2ccccc2)nc(N)n1
  OpenEye OEToolkits 1.5.0: c1ccc(cc1)CSc2cc(nc(n2)N)N
• Formula: C11 H12 N4 S
• Name: 6-(benzylsulfanyl)pyrimidine-2,4-diamine
• ChEMBL: CHEMBL566948
• ZINC: ZINC000001670209
• PDB chain: 3bmq Chain A Residue 270

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3bmq Structure-based design of pteridine reductase inhibitors targeting african sleeping sickness and the leishmaniases.
• Resolution: 1.7 Å
• Binding residue (original residue number in PDB): S95 F97 Y174 L208 P210 M213
• Binding residue (residue number reindexed from 1): S94 F96 Y159 L193 P195 M198
• Annotation score: 1
• Binding affinity: MOAD: Ki=3.2uM
  PDBbind-CN: -logKd/Ki=5.49,Ki=3.2uM

Enzymatic activity

• Catalytic site (original residue number in PDB): R14 D161 Y174 K178
• Catalytic site (residue number reindexed from 1): R13 D146 Y159 K163

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0016491 oxidoreductase activity
• GO:0047040 pteridine reductase activity

External links

• PDB: RCSB:3bmq, PDBe:3bmq, PDBj:3bmq
• PDBsum: 3bmq
• PubMed: 19916554
• UniProt: O76290