scPDB - 4dij entry

Protein Data Bank Entry:

PDB ID : 4dij

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2012-01-31

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	82 %
B	18 %

Ligand binding site composition:

B-Factor:	16.801
Number of residues:	34
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.086	637.875

% Hydrophobic	% Polar
51.85	48.15
According to VolSite

Ligand :

HET Code:	BLF
Formula:	C31H30Cl2N5O2
Molecular weight:	575.508 g/mol
DrugBank ID:	-
Buried Surface Area:	58.28 %
Polar Surface area:	76.38 Å2

Number of
H-Bond Acceptors:	3
H-Bond Donors:	3
Rings:	6
Aromatic rings:	5
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
10.1009	-3.63277	16.0868

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
N6	O	LEU- 54	2.78	155.74	H-Bond (Ligand Donor)	false
C41	CD1	LEU- 54	3.68	0	Hydrophobic	false
C3	CD1	LEU- 54	3.64	0	Hydrophobic	false
C3	CB	LEU- 57	3.77	0	Hydrophobic	false
C2	CD1	ILE- 61	3.59	0	Hydrophobic	false
C13	CD1	ILE- 61	3.67	0	Hydrophobic	false
C26	CG2	ILE- 61	3.48	0	Hydrophobic	false
C24	CE	MET- 62	4.14	0	Hydrophobic	false
C28	CB	TYR- 67	4.11	0	Hydrophobic	false
C64	CB	GLN- 72	4.09	0	Hydrophobic	false
CL1	CE2	PHE- 86	3.83	0	Hydrophobic	false
CL1	CZ	PHE- 91	3.95	0	Hydrophobic	false
C11	CG1	VAL- 93	3.64	0	Hydrophobic	false
C30	CG1	VAL- 93	3.72	0	Hydrophobic	false
DuAr	DuAr	HIS- 96	3.92	0	Aromatic Face/Face	false
CL2	CB	HIS- 96	3.8	0	Hydrophobic	false
CL2	CG2	ILE- 99	3.68	0	Hydrophobic	false
C13	CD1	ILE- 99	4.05	0	Hydrophobic	false
CL1	CG2	ILE- 99	3.79	0	Hydrophobic	false
C38	CD1	ILE- 99	3.74	0	Hydrophobic	false
CL2	CE1	TYR- 100	3.8	0	Hydrophobic	false