Structure of PDB 3lkj Chain C Binding Site BS01

Receptor Information
>3lkj Chain C (length=129) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QIAAHVISEASSKTTSVLQWAEKGYYTMSNNLVTLENGKQLTVKRQGLYY
IYAQVTFCSNPFIASLCLKSPGRFERILLRAANTPCGQQSIHLGGVFELQ
PGASVFVNVTDPSQVSHGTGFTSFGLLKL
Ligand information
Ligand IDLKJ
InChIInChI=1S/C53H60N8O6/c62-49(54-33-36-14-11-19-39(28-36)37-15-3-1-4-16-37)44-29-40(31-46(55-44)51(64)60-26-12-20-42(60)34-58-22-7-8-23-58)41-30-45(50(63)57-48(53(66)67)38-17-5-2-6-18-38)56-47(32-41)52(65)61-27-13-21-43(61)35-59-24-9-10-25-59/h1,3-4,9-11,14-16,19,24-25,28-32,38,42-43,48H,2,5-8,12-13,17-18,20-23,26-27,33-35H2,(H,54,62)(H,57,63)(H,66,67)/t42-,43-,48-/m1/s1
InChIKeyOURBCKKEKMWLAJ-JYIFATIISA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C(O)C(NC(=O)c3nc(C(=O)N2C(Cn1cccc1)CCC2)cc(c3)c6cc(nc(C(=O)NCc5cccc(c4ccccc4)c5)c6)C(=O)N7CCCC7CN8CCCC8)C9CCCCC9
OpenEye OEToolkits 1.7.0c1ccc(cc1)c2cccc(c2)CNC(=O)c3cc(cc(n3)C(=O)N4CCC[C@@H]4CN5CCCC5)c6cc(nc(c6)C(=O)N7CCC[C@@H]7Cn8cccc8)C(=O)N[C@H](C9CCCCC9)C(=O)O
CACTVS 3.370OC(=O)[CH](NC(=O)c1cc(cc(n1)C(=O)N2CCC[CH]2Cn3cccc3)c4cc(nc(c4)C(=O)N5CCC[CH]5CN6CCCC6)C(=O)NCc7cccc(c7)c8ccccc8)C9CCCCC9
CACTVS 3.370OC(=O)[C@H](NC(=O)c1cc(cc(n1)C(=O)N2CCC[C@@H]2Cn3cccc3)c4cc(nc(c4)C(=O)N5CCC[C@@H]5CN6CCCC6)C(=O)NCc7cccc(c7)c8ccccc8)C9CCCCC9
OpenEye OEToolkits 1.7.0c1ccc(cc1)c2cccc(c2)CNC(=O)c3cc(cc(n3)C(=O)N4CCCC4CN5CCCC5)c6cc(nc(c6)C(=O)N7CCCC7Cn8cccc8)C(=O)NC(C9CCCCC9)C(=O)O
FormulaC53 H60 N8 O6
Name(2R)-{[(2'-[(biphenyl-3-ylmethyl)carbamoyl]-6'-{[(2R)-2-(pyrrolidin-1-ylmethyl)pyrrolidin-1-yl]carbonyl}-6-{[(2R)-2-(1H-pyrrol-1-ylmethyl)pyrrolidin-1-yl]carbonyl}-4,4'-bipyridin-2-yl)carbonyl]amino}(cyclohexyl)ethanoic acid
ChEMBL
DrugBank
ZINCZINC000150344446
PDB chain3lkj Chain C Residue 1 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3lkj Small Molecule Inhibition of the TNF Family Cytokine CD40 Ligand through a Subunit Fracture Mechanism.
Resolution2.5 Å
Binding residue
(original residue number in PDB)		Q121 H125 Y145 Y146 Y170 Y172 H224 L259
Binding residue
(residue number reindexed from 1)		Q1 H5 Y25 Y26 Y50 Y52 H92 L127
Annotation score1
Binding affinityMOAD: ic50=25uM
PDBbind-CN: -logKd/Ki=4.60,IC50=25uM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0005164 tumor necrosis factor receptor binding
Biological Process
GO:0006955 immune response
Cellular Component
GO:0016020 membrane

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3lkj, PDBe:3lkj, PDBj:3lkj
PDBsum3lkj
PubMed21417339
UniProtP29965|CD40L_HUMAN CD40 ligand (Gene Name=CD40LG)

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