Structure of PDB 5ml8 Chain B Binding Site BS01

Receptor Information
>5ml8 Chain B (length=143) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SAKDERAREILRGFKLNWMNLRDAETGKILWQGTEDLSVPGVEHEARVPK
KILKCKAVSRELNFSSTEQMEKFRLEQKVYFKGQCLEEWFFEFGFVIPNS
TNTWQSLIEMMPASVLTGNVIIETKFFDDDLLVSTSRVRLFYV
Ligand information
Ligand IDV98
InChIInChI=1S/C31H38ClN3O4S2/c32-28-12-10-26(11-13-28)24-35(29-8-4-5-9-29)41(38,39)31-16-14-30(15-17-31)40(36,37)34(22-25-6-2-1-3-7-25)23-27-18-20-33-21-19-27/h1-3,6-7,10-17,27,29,33H,4-5,8-9,18-24H2
InChIKeySCLQBRLPJHXGKJ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6c1ccc(cc1)CN(CC2CCNCC2)S(=O)(=O)c3ccc(cc3)S(=O)(=O)N(Cc4ccc(cc4)Cl)C5CCCC5
CACTVS 3.385Clc1ccc(CN(C2CCCC2)[S](=O)(=O)c3ccc(cc3)[S](=O)(=O)N(CC4CCNCC4)Cc5ccccc5)cc1
FormulaC31 H38 Cl N3 O4 S2
Name~{N}4-[(4-chlorophenyl)methyl]-~{N}4-cyclopentyl-~{N}1-(phenylmethyl)-~{N}1-(piperidin-4-ylmethyl)benzene-1,4-disulfonamide
ChEMBL
DrugBank
ZINCZINC000584905712
PDB chain5ml8 Chain B Residue 201 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5ml8 A PDE6 delta-KRas Inhibitor Chemotype with up to Seven H-Bonds and Picomolar Affinity that Prevents Efficient Inhibitor Release by Arl2.
Resolution2.6 Å
Binding residue
(original residue number in PDB)		M20 L22 W32 I53 C56 R61 Q78 E88 W90 M117 I129 T131 L147 Y149
Binding residue
(residue number reindexed from 1)		M19 L21 W31 I52 C55 R60 Q77 E87 W89 M110 I122 T124 L140 Y142
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=8.10,Kd=8nM
BindingDB: Kd=16nM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0005095 GTPase inhibitor activity
GO:0005515 protein binding
GO:0031267 small GTPase binding
Biological Process
GO:0007601 visual perception
GO:0050953 sensory perception of light stimulus
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005856 cytoskeleton
GO:0005929 cilium
GO:0016020 membrane
GO:0030659 cytoplasmic vesicle membrane
GO:0031410 cytoplasmic vesicle
GO:0042995 cell projection

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5ml8, PDBe:5ml8, PDBj:5ml8
PDBsum5ml8
PubMed28106325
UniProtO43924|PDE6D_HUMAN Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta (Gene Name=PDE6D)

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