scPDB - 4jwr entry

Protein Data Bank Entry:

PDB ID : 4jwr

Resolution :2.350 Å

Experimental Method : X-ray

Deposition Date : 2013-03-27

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	E3 ubiquitin-protein ligase Mdm2
ID:	MDM2_HUMAN
AC:	Q00987
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	6.3.2

Chains:

Chain Name:	Percentage of Residues within binding site
A	96 %
B	4 %

Ligand binding site composition:

B-Factor:	32.355
Number of residues:	27
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.525	462.375

% Hydrophobic	% Polar
68.61	31.39
According to VolSite

Ligand :

HET Code:	1MY
Formula:	C22H22Cl2NO5
Molecular weight:	451.320 g/mol
DrugBank ID:	-
Buried Surface Area:	53.03 %
Polar Surface area:	89.9 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	1
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
7.14047	-11.5767	-0.7716

Binding mode :

What is Poseview ?

2D View
3D View

Image generated by PoseView

Protein

Binding Site

Ligand

Interaction pattern

hydrophobic (CA)

aromatic (CZ)

hydrogen bond acceptor (O)

hydrogen bond acceptor/donor (OG)

hydrogen bond donor (N)

positively ionized (NZ)

negatively ionized (OD1)

metal (ZN)

Legend:

Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand

Image generated using PoseView by BioSolveIT

Ligand	Protein		Interaction
Atom	Atom	Residue	Distance (Å)	Angle (°)	Type
CL2	CD1	LEU- 54	3.93	0	Hydrophobic	false
C17	CG	LEU- 54	4.11	0	Hydrophobic	false
C18	CD1	LEU- 54	3.6	0	Hydrophobic	false
C12	CD1	LEU- 54	3.68	0	Hydrophobic	false
CL1	CB	LEU- 57	3.87	0	Hydrophobic	false
C12	CB	LEU- 57	4.05	0	Hydrophobic	false
C4	CG2	ILE- 61	3.86	0	Hydrophobic	false
C13	CD1	ILE- 61	3.88	0	Hydrophobic	false
C3	SD	MET- 62	3.77	0	Hydrophobic	false
CL1	CZ	PHE- 86	3.92	0	Hydrophobic	false
CL1	CZ	PHE- 91	4.45	0	Hydrophobic	false
C7	CB	VAL- 93	4.06	0	Hydrophobic	false
C4	CG1	VAL- 93	4.21	0	Hydrophobic	false
C15	CG1	VAL- 93	4.41	0	Hydrophobic	false
O5	NE2	HIS- 96	3.2	153.12	H-Bond (Protein Donor)	false
CL2	CB	HIS- 96	3.56	0	Hydrophobic	false
CL2	CG2	ILE- 99	3.51	0	Hydrophobic	false
C14	CD1	ILE- 99	4.1	0	Hydrophobic	false
CL1	CG2	ILE- 99	3.78	0	Hydrophobic	false
CL2	CE1	TYR- 100	3.92	0	Hydrophobic	false
CL1	CD1	ILE- 103	4.43	0	Hydrophobic	false