Structure of PDB 3lmy Chain A Binding Site BS01

Receptor Information
>3lmy Chain A (length=479) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PALWPLPLSVKMTPNLLHLAPENFYISHSPNSTAGPSCTLLEEAFRRYHG
YIFTQVQQLLVSITLQSECDAFPNISSDESYTLLVKEPVAVLKANRVWGA
LRGLETFSQLVYQDSYGTFTINESTIIDSPRFSHRGILIDTSRHYLPVKI
ILKTLDAMAFNKFNVLHWHIVDDQSFPYQSITFPELSNKGSYSLSHVYTP
NDVRMVIEYARLRGIRVLPEFDTPGHTLSWGKGQKDLLTPCYSDSFGPIN
PTLNTTYSFLTTFFKEISEVFPDQFIHLGGDEVEFKCWESNPKIQDFMRQ
KGFGTDFKKLESFYIQKVLDIIATINKGSIVWQEVFDDKAKLAPGTIVEV
WKDSAYPEELSRVTASGFPVILSAPWYLDLISYGQDWRKYYKVEPLDFGG
TQKQKQLFIGGEACLWGEYVDATNLTPRLWPRASAVGERLWSSKDVRDMD
DAYDRLTRHRCRMVERGIAAQPLYAGYCN
Ligand information
Ligand IDCP6
InChIInChI=1S/C12H13ClN4/c1-2-9-10(11(14)17-12(15)16-9)7-3-5-8(13)6-4-7/h3-6H,2H2,1H3,(H4,14,15,16,17)
InChIKeyWKSAUQYGYAYLPV-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CCc1c(c(nc(n1)N)N)c2ccc(cc2)Cl
ACDLabs 10.04Clc2ccc(c1c(nc(nc1CC)N)N)cc2
CACTVS 3.341CCc1nc(N)nc(N)c1c2ccc(Cl)cc2
FormulaC12 H13 Cl N4
Name5-(4-CHLORO-PHENYL)-6-ETHYL-PYRIMIDINE-2,4-DIAMINE;
PYRIMETHAMINE
ChEMBLCHEMBL36
DrugBankDB00205
ZINCZINC000000057464
PDB chain3lmy Chain A Residue 562 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3lmy The Crystal Structure of beta-hexosaminidase B in complex with Pyrimethamine
Resolution2.8 Å
Binding residue
(original residue number in PDB)		R211 H294 D354 W424 Y450 L453 W489 E491
Binding residue
(residue number reindexed from 1)		R143 H226 D281 W351 Y377 L380 W416 E418
Annotation score1
Binding affinityBindingDB: IC50=9100nM
Enzymatic activity
Catalytic site (original residue number in PDB) D354 E355
Catalytic site (residue number reindexed from 1) D281 E282
Enzyme Commision number 3.2.1.52: beta-N-acetylhexosaminidase.
Gene Ontology
Molecular Function
GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds
GO:0004563 beta-N-acetylhexosaminidase activity
Biological Process
GO:0005975 carbohydrate metabolic process

View graph for
Molecular Function
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Biological Process
External links
PDB RCSB:3lmy, PDBe:3lmy, PDBj:3lmy
PDBsum3lmy
PubMed
UniProtP07686|HEXB_HUMAN Beta-hexosaminidase subunit beta (Gene Name=HEXB)

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