Structure of PDB 5ml3 Chain B Binding Site BS01

Receptor Information
>5ml3 Chain B (length=149) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SAKDERAREILRGFKLNWMNLRDAETGKILWQGTEDLSVPGVEHEARVPK
KILKCKAVSRELNFSSTEQMEKFRLEQKVYFKGQCLEEWFFEFGFVIPNS
TNTWQSLIEAAPESQMMPASVLTGNVIIETKFFDDDLLVSTSRVRLFYV
Ligand information
Ligand IDDL3
InChIInChI=1S/C30H39ClN6O4S2/c1-32-30-34-19-16-26(35-30)22-36(20-24-14-17-33-18-15-24)42(38,39)28-10-12-29(13-11-28)43(40,41)37(27-4-2-3-5-27)21-23-6-8-25(31)9-7-23/h6-13,16,19,24,27,33H,2-5,14-15,17-18,20-22H2,1H3,(H,32,34,35)
InChIKeyFWBBCSKXUXMTJY-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CNc1nccc(CN(CC2CCNCC2)[S](=O)(=O)c3ccc(cc3)[S](=O)(=O)N(Cc4ccc(Cl)cc4)C5CCCC5)n1
OpenEye OEToolkits 2.0.6CNc1nccc(n1)CN(CC2CCNCC2)S(=O)(=O)c3ccc(cc3)S(=O)(=O)N(Cc4ccc(cc4)Cl)C5CCCC5
FormulaC30 H39 Cl N6 O4 S2
Name~{N}1-[(4-chlorophenyl)methyl]-~{N}1-cyclopentyl-~{N}4-[[2-(methylamino)pyrimidin-4-yl]methyl]-~{N}4-(piperidin-4-ylmethyl)benzene-1,4-disulfonamide
ChEMBLCHEMBL4472979
DrugBank
ZINCZINC000584905549
PDB chain5ml3 Chain B Residue 201 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5ml3 A PDE6 delta-KRas Inhibitor Chemotype with up to Seven H-Bonds and Picomolar Affinity that Prevents Efficient Inhibitor Release by Arl2.
Resolution1.4 Å
Binding residue
(original residue number in PDB)		M20 L22 W32 I53 C56 R61 Q78 W90 I109 M117 I129 T131 F133 L147 Y149
Binding residue
(residue number reindexed from 1)		M19 L21 W31 I52 C55 R60 Q77 W89 I108 M116 I128 T130 F132 L146 Y148
Annotation score1
Binding affinityMOAD: Kd=203pM
PDBbind-CN: -logKd/Ki=9.69,Kd=203pM
BindingDB: Kd=203nM
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:5ml3, PDBe:5ml3, PDBj:5ml3
PDBsum5ml3
PubMed28106325
UniProtO43924|PDE6D_HUMAN Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta (Gene Name=PDE6D)

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