scPDB - 4ago entry

Protein Data Bank Entry:

PDB ID : 4ago

Resolution :1.450 Å

Experimental Method : X-ray

Deposition Date : 2012-01-30

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Cellular tumor antigen p53
ID:	P53_HUMAN
AC:	P04637
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	9.681
Number of residues:	23
Including
Standard Amino Acids:	20
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.789	459.000

% Hydrophobic	% Polar
42.65	57.35
According to VolSite

Ligand :

HET Code:	P74
Formula:	C24H38IN3O3
Molecular weight:	543.481 g/mol
DrugBank ID:	-
Buried Surface Area:	41.54 %
Polar Surface area:	67.44 Å2

Number of
H-Bond Acceptors:	3
H-Bond Donors:	4
Rings:	2
Aromatic rings:	1
Anionic atoms:	0
Cationic atoms:	2
Rule of Five Violation:	1
Rotatable Bonds:	10

Mass center Coordinates

X	Y	Z
90.9616	95.9989	-46.2095

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
I2	CB	LEU- 145	4.21	0	Hydrophobic	false
C15	CG2	VAL- 147	4.06	0	Hydrophobic	false
I2	CG2	VAL- 147	3.99	0	Hydrophobic	false
C7	CG2	VAL- 147	3.52	0	Hydrophobic	false
C4	CG2	VAL- 147	3.58	0	Hydrophobic	false
C3	CG2	THR- 150	3.72	0	Hydrophobic	false
C04	CG2	THR- 150	3.99	0	Hydrophobic	false
C17	CG2	THR- 150	4.17	0	Hydrophobic	false
N	O	PRO- 151	2.9	141.93	H-Bond (Ligand Donor)	false
C04	CG	PRO- 151	4.32	0	Hydrophobic	false
C	CG	PRO- 153	4.3	0	Hydrophobic	false
C02	SG	CYS- 220	3.91	0	Hydrophobic	false
C04	SG	CYS- 220	4.07	0	Hydrophobic	false
C17	CG	PRO- 222	3.83	0	Hydrophobic	false
C04	CG	PRO- 222	3.92	0	Hydrophobic	false
C3	CB	PRO- 222	3.76	0	Hydrophobic	false
C7	CG	PRO- 223	4.05	0	Hydrophobic	false
I2	CB	THR- 230	4.01	0	Hydrophobic	false
O1	O	HOH- 2094	3	179.95	H-Bond (Protein Donor)	false