Structure of PDB 6ggn Chain A Binding Site BS01

Receptor Information
>6ggn Chain A (length=94) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QIPASEQETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLY
DEKQQHIVYCSNDLLGDLFGVPSFSVKEHRKIYTMIYRNLVVVN
Ligand information
Ligand IDEYH
InChIInChI=1S/C28H27Cl2N5O3/c1-14(2)34-24-22(32-25(34)20-13-31-28(38-6)33-26(20)37-5)27(36)35(21-12-18(30)8-7-15(21)3)23(24)19-10-9-17(29)11-16(19)4/h7-14,23H,1-6H3/t23-/m0/s1
InChIKeyXBJHBEQDHSREQB-QHCPKHFHSA-N
SMILES
SoftwareSMILES
CACTVS 3.385COc1ncc(c(OC)n1)c2nc3C(=O)N([CH](c4ccc(Cl)cc4C)c3n2C(C)C)c5cc(Cl)ccc5C
OpenEye OEToolkits 2.0.6Cc1ccc(cc1N2C(c3c(nc(n3C(C)C)c4cnc(nc4OC)OC)C2=O)c5ccc(cc5C)Cl)Cl
OpenEye OEToolkits 2.0.6Cc1ccc(cc1N2[C@H](c3c(nc(n3C(C)C)c4cnc(nc4OC)OC)C2=O)c5ccc(cc5C)Cl)Cl
CACTVS 3.385COc1ncc(c(OC)n1)c2nc3C(=O)N([C@@H](c4ccc(Cl)cc4C)c3n2C(C)C)c5cc(Cl)ccc5C
FormulaC28 H27 Cl2 N5 O3
Name(4~{S})-4-(4-chloranyl-2-methyl-phenyl)-5-(5-chloranyl-2-methyl-phenyl)-2-(2,4-dimethoxypyrimidin-5-yl)-3-propan-2-yl-4~{H}-pyrrolo[3,4-d]imidazol-6-one
ChEMBLCHEMBL3653231
DrugBank
ZINCZINC000169705372
PDB chain6ggn Chain A Residue 201 [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]
PDB6ggn In vitro and in vivo characterization of a novel, highly potent p53-MDM2 inhibitor.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		L54 G58 I61 M62 Y67 Q72 F86 V93 H96 I99 Y100
Binding residue
(residue number reindexed from 1)		L37 G41 I44 M45 Y50 Q55 F69 V76 H79 I82 Y83
Annotation score1
Binding affinityMOAD: ic50=0.08nM
PDBbind-CN: -logKd/Ki=10.10,IC50=0.08nM
BindingDB: IC50=0.17nM
Enzymatic activity
Enzyme Commision number 2.3.2.27: RING-type E3 ubiquitin transferase.
Gene Ontology
Biological Process
GO:0043066 negative regulation of apoptotic process
GO:0051726 regulation of cell cycle
Cellular Component
GO:0005634 nucleus

View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6ggn, PDBe:6ggn, PDBj:6ggn
PDBsum6ggn
PubMed30217415
UniProtQ00987|MDM2_HUMAN E3 ubiquitin-protein ligase Mdm2 (Gene Name=MDM2)

[Back to BioLiP]