Structure of PDB 5vkc Chain A Binding Site BS01

Receptor Information
>5vkc Chain A (length=144) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MDLYRQSLEIISRYLREQATGAKSGATSRKALETLRRVGDGVQRNHETAF
QGMLRKLDIKNEDDVKSLSRVMIHVFSDGVTNWGRIVTLISFGAFVAKHL
KTINQESCIEPLAESITDVLVRTKRDWLVKQRGWDGFVEFFHVE
Ligand information
Ligand ID9EA
InChIInChI=1S/C46H46N6O5/c1-31-43(41(48-49(31)3)30-57-36-20-18-35(19-21-36)51-25-23-50(24-26-51)32(2)53)40-15-7-14-38-39(16-9-27-56-42-17-6-12-34-11-4-5-13-37(34)42)45(46(54)55)52(44(38)40)29-33-10-8-22-47-28-33/h4-8,10-15,17-22,28H,9,16,23-27,29-30H2,1-3H3,(H,54,55)
InChIKeyVKKQBUSCPZGZBT-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Cn1nc(COc2ccc(cc2)N3CCN(CC3)C(C)=O)c(c1C)c4cccc5c(CCCOc6cccc7ccccc67)c(n(Cc8cccnc8)c45)C(O)=O
OpenEye OEToolkits 2.0.6Cc1c(c(nn1C)COc2ccc(cc2)N3CCN(CC3)C(=O)C)c4cccc5c4n(c(c5CCCOc6cccc7c6cccc7)C(=O)O)Cc8cccnc8
ACDLabs 12.01c2cc(c1ccccc1c2)OCCCc7c6cccc(c3c(n(C)nc3COc4ccc(cc4)N5CCN(C(C)=O)CC5)C)c6n(c7C(O)=O)Cc8cnccc8
FormulaC46 H46 N6 O5
Name7-(3-{[4-(4-acetylpiperazin-1-yl)phenoxy]methyl}-1,5-dimethyl-1H-pyrazol-4-yl)-3-{3-[(naphthalen-1-yl)oxy]propyl}-1-[(pyridin-3-yl)methyl]-1H-indole-2-carboxylic acid
ChEMBLCHEMBL3417706
DrugBank
ZINCZINC000164088109
PDB chain5vkc Chain A 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]
PDB5vkc Structure-guided design of a series of MCL-1 inhibitors with high affinity and selectivity.
Resolution2.31 Å
Binding residue
(original residue number in PDB)		V220 H224 A227 F228 M231 M250 V253 G262 R263 T266 L267 F270
Binding residue
(residue number reindexed from 1)		V42 H46 A49 F50 M53 M72 V75 G84 R85 T88 L89 F92
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=8.74,Ki=1.8nM
BindingDB: Ki=98nM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Biological Process
GO:0042981 regulation of apoptotic process

View graph for
Biological Process
External links
PDB RCSB:5vkc, PDBe:5vkc, PDBj:5vkc
PDBsum5vkc
PubMed25679114
UniProtQ07820|MCL1_HUMAN Induced myeloid leukemia cell differentiation protein Mcl-1 (Gene Name=MCL1)

[Back to BioLiP]