Structure of PDB 5ml4 Chain B Binding Site BS01

Receptor Information
>5ml4 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 IDRRQ
InChIInChI=1S/C33H41ClN4O6S2/c1-35-32-20-26(8-15-31(32)33(39)40)22-37(21-25-16-18-36-19-17-25)45(41,42)29-11-13-30(14-12-29)46(43,44)38(28-4-2-3-5-28)23-24-6-9-27(34)10-7-24/h6-15,20,25,28,35-36H,2-5,16-19,21-23H2,1H3,(H,39,40)
InChIKeyAAUHXDBDDJEFRE-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CNc1cc(CN(CC2CCNCC2)[S](=O)(=O)c3ccc(cc3)[S](=O)(=O)N(Cc4ccc(Cl)cc4)C5CCCC5)ccc1C(O)=O
OpenEye OEToolkits 2.0.6CNc1cc(ccc1C(=O)O)CN(CC2CCNCC2)S(=O)(=O)c3ccc(cc3)S(=O)(=O)N(Cc4ccc(cc4)Cl)C5CCCC5
FormulaC33 H41 Cl N4 O6 S2
Name4-[[[4-[(4-chlorophenyl)methyl-cyclopentyl-sulfamoyl]phenyl]sulfonyl-(piperidin-4-ylmethyl)amino]methyl]-2-(methylamino)benzoic acid
ChEMBL
DrugBank
ZINCZINC000584905648
PDB chain5ml4 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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PDB5ml4 A PDE6 delta-KRas Inhibitor Chemotype with up to Seven H-Bonds and Picomolar Affinity that Prevents Efficient Inhibitor Release by Arl2.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		M20 L22 W32 I53 L54 C56 R61 Q78 E88 W90 M117 L123 I129 T131 L147 Y149
Binding residue
(residue number reindexed from 1)		M19 L21 W31 I52 L53 C55 R60 Q77 E87 W89 M116 L122 I128 T130 L146 Y148
Annotation score1
Binding affinityMOAD: Kd<2nM
PDBbind-CN: -logKd/Ki=8.70,Kd<2nM
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:5ml4, PDBe:5ml4, PDBj:5ml4
PDBsum5ml4
PubMed28106325
UniProtO43924|PDE6D_HUMAN Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta (Gene Name=PDE6D)

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