Structure of PDB 8sz3 Chain B Binding Site BS01

Receptor Information
>8sz3 Chain B (length=323) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EAYWNREQEKLNRQYNPILSSHLNYCEPDLRVTSVVTGFNNLPDRFKDFL
LYLRCRNYSLLIDQPDKCAKKPFLLLAIKSLTPHFARRQAIRESWGQESQ
TVVRVFLLGQTPPEDNHPDLSDMLKFESEKHQDILMWNYRDTFFNLSLKE
VLFLRWVSTSCPDTEFVFKGDDDVFVNTHHILNYLNSLSKTKAKDLFIGD
VIHNAGPHRDKKLKYYIPEVVYSGLYPPYAGGGGFLYSGHLALRLYHITD
QVHLYPIDDVYTGMCLQKLGLVPEKHKGFRTFDIEEKNKNNICSYVDLML
VHSRKPQEMIDIWSQLQSAHLKC
Ligand information
Ligand IDX18
InChIInChI=1S/C21H25BrN4O2/c1-12(16-9-7-15(22)11-23-16)24-19(27)14-6-8-17-18(10-14)26(20(28)25-17)13(2)21(3,4)5/h6-13H,1-5H3,(H,24,27)(H,25,28)/t12-,13+/m0/s1
InChIKeyDLMZWVVEARAWSJ-QWHCGFSZSA-N
SMILES
SoftwareSMILES
CACTVS 3.385C[C@H](NC(=O)c1ccc2NC(=O)N([C@H](C)C(C)(C)C)c2c1)c3ccc(Br)cn3
ACDLabs 12.01Brc1ccc(nc1)C(C)NC(=O)c1ccc2NC(=O)N(c2c1)C(C)C(C)(C)C
CACTVS 3.385C[CH](NC(=O)c1ccc2NC(=O)N([CH](C)C(C)(C)C)c2c1)c3ccc(Br)cn3
OpenEye OEToolkits 2.0.7CC(c1ccc(cn1)Br)NC(=O)c2ccc3c(c2)N(C(=O)N3)C(C)C(C)(C)C
OpenEye OEToolkits 2.0.7C[C@@H](c1ccc(cn1)Br)NC(=O)c2ccc3c(c2)N(C(=O)N3)[C@H](C)C(C)(C)C
FormulaC21 H25 Br N4 O2
NameN-[(1S)-1-(5-bromopyridin-2-yl)ethyl]-3-[(2R)-3,3-dimethylbutan-2-yl]-2-oxo-2,3-dihydro-1H-benzimidazole-5-carboxamide
ChEMBL
DrugBank
ZINC
PDB chain8sz3 Chain B Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB8sz3 Imidazolone as an Amide Bioisostere in the Development of beta-1,3- N -Acetylglucosaminyltransferase 2 (B3GNT2) Inhibitors.
Resolution2.32 Å
Binding residue
(original residue number in PDB)		R115 K149 S150 L151 D215 T216 F217 L220 K223 D245 D246 K288
Binding residue
(residue number reindexed from 1)		R45 K79 S80 L81 D141 T142 F143 L146 K149 D171 D172 K214
Annotation score1
Enzymatic activity
Enzyme Commision number 2.4.1.149: N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase.
Gene Ontology
Molecular Function
GO:0005515 protein binding
GO:0008499 UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity
GO:0008532 N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase activity
GO:0016757 glycosyltransferase activity
GO:0016758 hexosyltransferase activity
Biological Process
GO:0006486 protein glycosylation
GO:0006493 protein O-linked glycosylation
GO:0007411 axon guidance
GO:0007608 sensory perception of smell
GO:0016266 O-glycan processing
GO:0018146 keratan sulfate biosynthetic process
GO:0030311 poly-N-acetyllactosamine biosynthetic process
GO:1990830 cellular response to leukemia inhibitory factor
Cellular Component
GO:0000139 Golgi membrane
GO:0005794 Golgi apparatus
GO:0016020 membrane

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8sz3, PDBe:8sz3, PDBj:8sz3
PDBsum8sz3
PubMed37988652
UniProtQ9NY97|B3GN2_HUMAN N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase 2 (Gene Name=B3GNT2)

[Back to BioLiP]