Structure of PDB 5qth Chain A Binding Site BS01

Receptor Information

>5qth Chain A (length=329) Species: 5691 (Trypanosoma brucei)

MPMQMFMQVYDEIQMFLLEELELKFDMDPNRVRYLRKMMDTTCLGGKYNR
GLTVIDVAESLLSLSGARRKRVLHDACVCGWMIEFLQAHYLVEDDIMDNH
PDVTVQCAINDGLLLKSWTHMMAMHFFADRPFLQDLLCRFNRVDYTTAVG
QLYDVTSMFDSNDFAEFTLSNYKRIVKYKTAYYTYLLPLVMGLIVSEALP
TVDMGVTEELAMLMGEYFQVQDDVMDCFTPPERLGKVGTDIQDAKCSWLA
VTFLAKASSAQVAEFKANYGSGDSEKVATVRRLYEEADLQGDYVAYEAAV
AEQVKELIEKLRLCSPGFAASVETLWGKT

Ligand information

• Ligand ID: PJY
• InChI: InChI=1S/C9H12N2OS/c1-11(2)9(12)7-5-4-6-10-8(7)13-3/h4-6H,1-3H3
• InChIKey: KORZBTDVYBSAMM-UHFFFAOYSA-N
• SMILES:
  ACDLabs 12.01: CSc1c(cccn1)C(=O)N(C)C
  CACTVS 3.385: CSc1ncccc1C(=O)N(C)C
  OpenEye OEToolkits 2.0.6: CN(C)C(=O)c1cccnc1SC
• Formula: C9 H12 N2 O S
• Name: N,N-dimethyl-2-(methylsulfanyl)pyridine-3-carboxamide
• ZINC: ZINC000000092203
• PDB chain: 5qth Chain A Residue 404

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5qth T. brucei FPPS in complex with CID 2799882
• Resolution: 1.887 Å
• Binding residue (original residue number in PDB): N49 R50 T217 F251 L358 K361 T362
• Binding residue (residue number reindexed from 1): N49 R50 T184 F218 L325 K328 T329
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): K47 H98 D103 D107 D175 K212 F251 D255 D256
• Catalytic site (residue number reindexed from 1): K47 H89 D94 D98 D154 K179 F218 D222 D223

Gene Ontology

Molecular Function

• GO:0004161 dimethylallyltranstransferase activity
• GO:0004337 geranyltranstransferase activity
• GO:0004659 prenyltransferase activity
• GO:0016740 transferase activity
• GO:0016765 transferase activity, transferring alkyl or aryl (other than methyl) groups
• GO:0046872 metal ion binding

Biological Process

• GO:0008299 isoprenoid biosynthetic process
• GO:0045337 farnesyl diphosphate biosynthetic process

Cellular Component

• GO:0005737 cytoplasm

External links

• PDB: RCSB:5qth, PDBe:5qth, PDBj:5qth
• PDBsum: 5qth
• UniProt: Q86C09