scPDB - 4man entry

Protein Data Bank Entry:

PDB ID : 4man

Resolution :2.070 Å

Experimental Method : X-ray

Deposition Date : 2013-08-16

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Apoptosis regulator Bcl-2
ID:	BCL2_HUMAN
AC:	P10415
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:	32.604
Number of residues:	41
Including
Standard Amino Acids:	40
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.605	367.875

% Hydrophobic	% Polar
60.55	39.45
According to VolSite

Ligand :

HET Code:	1Y1
Formula:	C48H54ClN7O8S
Molecular weight:	924.502 g/mol
DrugBank ID:	-
Buried Surface Area:	50.82 %
Polar Surface area:	185.06 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	5
Rings:	8
Aromatic rings:	6
Anionic atoms:	1
Cationic atoms:	3
Rule of Five Violation:	3
Rotatable Bonds:	17

Mass center Coordinates

X	Y	Z
-11.7391	10.3003	8.85594

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
C41	CB	GLN- 96	4.07	0	Hydrophobic	false
C41	CB	ALA- 97	4.08	0	Hydrophobic	false
N49	OD1	ASP- 100	2.79	170.43	H-Bond (Ligand Donor)	false
C34	CB	ASP- 100	3.89	0	Hydrophobic	false
CL6	CE2	PHE- 101	3.95	0	Hydrophobic	false
C36	CE1	PHE- 101	4.29	0	Hydrophobic	false
C37	CE1	PHE- 101	4.05	0	Hydrophobic	false
C19	CB	PHE- 101	4.11	0	Hydrophobic	false
C6	CG	ARG- 104	4.34	0	Hydrophobic	false
C37	CE2	TYR- 105	3.67	0	Hydrophobic	false
C3	CB	ASP- 108	4.38	0	Hydrophobic	false
CL6	CD2	PHE- 109	3.39	0	Hydrophobic	false
C12	CB	MET- 112	3.52	0	Hydrophobic	false
C2	CE	MET- 112	3.84	0	Hydrophobic	false
C3	CE	MET- 112	3.57	0	Hydrophobic	false
C32	CG	MET- 112	4.05	0	Hydrophobic	false
C2	CG1	VAL- 130	3.83	0	Hydrophobic	false
C1	CB	GLU- 133	4.46	0	Hydrophobic	false
C9	CG	GLU- 133	4.24	0	Hydrophobic	false
C1	CB	LEU- 134	3.89	0	Hydrophobic	false
C36	CD1	LEU- 134	3.74	0	Hydrophobic	false
C2	CD1	LEU- 134	4.18	0	Hydrophobic	false
C7	CG	ARG- 143	3.93	0	Hydrophobic	false
C36	CB	ALA- 146	3.9	0	Hydrophobic	false
C4	CB	ALA- 146	4	0	Hydrophobic	false
CL6	CB	GLU- 149	4.08	0	Hydrophobic	false
C13	CB	PHE- 150	3.78	0	Hydrophobic	false
CL6	CG2	VAL- 153	4.36	0	Hydrophobic	false
C46	CD1	TYR- 199	3.89	0	Hydrophobic	false
C35	CB	TYR- 199	3.67	0	Hydrophobic	false