scPDB - 4hbm entry

Protein Data Bank Entry:

PDB ID : 4hbm

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2012-09-28

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	83 %
B	17 %

Ligand binding site composition:

B-Factor:	21.781
Number of residues:	38
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.262	675.000

% Hydrophobic	% Polar
53.00	47.00
According to VolSite

Ligand :

HET Code:	0Y7
Formula:	C23H24Cl2NO4
Molecular weight:	449.347 g/mol
DrugBank ID:	-
Buried Surface Area:	67.87 %
Polar Surface area:	80.67 Å2

Number of
H-Bond Acceptors:	4
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
18.9173	13.3021	16.3019

Binding mode :

What is Poseview ?

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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
C15	CG2	THR- 10	4.11	0	Hydrophobic	false
C19	CG2	VAL- 14	3.73	0	Hydrophobic	false
C19	CB	THR- 16	3.9	0	Hydrophobic	false
C20	CG2	THR- 16	3.51	0	Hydrophobic	false
C20	CG	LEU- 54	3.94	0	Hydrophobic	false
C4	CD1	LEU- 54	3.56	0	Hydrophobic	false
C21	CD1	LEU- 54	3.56	0	Hydrophobic	false
CL1	CB	LEU- 57	3.8	0	Hydrophobic	false
C23	CG2	ILE- 61	3.73	0	Hydrophobic	false
C2	CD1	ILE- 61	3.62	0	Hydrophobic	false
C10	SD	MET- 62	4.46	0	Hydrophobic	false
C23	CD1	TYR- 67	4.31	0	Hydrophobic	false
CL1	CZ	PHE- 86	3.82	0	Hydrophobic	false
C3	CB	VAL- 93	4.34	0	Hydrophobic	false
C13	CG2	VAL- 93	3.83	0	Hydrophobic	false
C23	CG1	VAL- 93	4.21	0	Hydrophobic	false
O2	NZ	LYS- 94	3.77	0	Ionic (Protein Cationic)	false
O3	NZ	LYS- 94	2.91	0	Ionic (Protein Cationic)	false
O3	NZ	LYS- 94	2.91	164.62	H-Bond (Protein Donor)	false
O2	NE2	HIS- 96	2.9	140.05	H-Bond (Protein Donor)	false
CL2	CB	HIS- 96	3.43	0	Hydrophobic	false
CL2	CG2	ILE- 99	3.91	0	Hydrophobic	false
C22	CD1	ILE- 99	4.47	0	Hydrophobic	false
CL1	CG2	ILE- 99	3.91	0	Hydrophobic	false
C2	CD1	ILE- 99	3.94	0	Hydrophobic	false
CL2	CE1	TYR- 100	3.67	0	Hydrophobic	false
O4	O	HOH- 305	2.82	161.85	H-Bond (Ligand Donor)	false