scPDB - 4lvt entry

Protein Data Bank Entry:

PDB ID : 4lvt

Resolution :2.050 Å

Experimental Method : X-ray

Deposition Date : 2013-07-26

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
B	100 %

Ligand binding site composition:

B-Factor:	26.441
Number of residues:	35
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.983	384.750

% Hydrophobic	% Polar
61.40	38.60
According to VolSite

Ligand :

HET Code:	1XJ
Formula:	C47H57ClF3N5O6S3
Molecular weight:	976.629 g/mol
DrugBank ID:	DB12340
Buried Surface Area:	50.48 %
Polar Surface area:	172.81 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	4
Rings:	7
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	2
Rule of Five Violation:	3
Rotatable Bonds:	17

Mass center Coordinates

X	Y	Z
25.9112	34.9942	32.7965

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
S62	CB	ASP- 100	3.68	0	Hydrophobic	false
C31	CE1	PHE- 101	4.38	0	Hydrophobic	false
C32	CE1	PHE- 101	4.23	0	Hydrophobic	false
CL6	CE2	PHE- 101	3.87	0	Hydrophobic	false
C11	CB	PHE- 101	3.95	0	Hydrophobic	false
C2	CB	PHE- 101	3.82	0	Hydrophobic	false
C32	CD2	TYR- 105	3.92	0	Hydrophobic	false
C8	CZ	TYR- 105	3.39	0	Hydrophobic	false
C4	CB	ASP- 108	4.15	0	Hydrophobic	false
CL6	CD2	PHE- 109	3.54	0	Hydrophobic	false
C28	CE	MET- 112	3.72	0	Hydrophobic	false
C14	CB	MET- 112	3.72	0	Hydrophobic	false
C41	CE	MET- 112	4.47	0	Hydrophobic	false
C4	CE	MET- 112	3.7	0	Hydrophobic	false
C28	CG1	VAL- 130	3.63	0	Hydrophobic	false
C40	CB	GLU- 133	4.06	0	Hydrophobic	false
C30	CB	LEU- 134	4.24	0	Hydrophobic	false
C31	CD1	LEU- 134	4.03	0	Hydrophobic	false
F59	CB	TRP- 141	3.81	0	Hydrophobic	false
O56	N	GLY- 142	3.11	141.15	H-Bond (Protein Donor)	false
C9	CG	ARG- 143	4.09	0	Hydrophobic	false
C1	CB	VAL- 145	4.45	0	Hydrophobic	false
C2	CG1	VAL- 145	3.8	0	Hydrophobic	false
C31	CB	ALA- 146	4.29	0	Hydrophobic	false
C5	CB	ALA- 146	4.26	0	Hydrophobic	false
CL6	CB	GLU- 149	4.03	0	Hydrophobic	false
C15	CB	PHE- 150	3.73	0	Hydrophobic	false
CL6	CG2	VAL- 153	3.66	0	Hydrophobic	false
C47	CE1	PHE- 195	4.24	0	Hydrophobic	false
F61	CD1	PHE- 195	3.43	0	Hydrophobic	false
F59	CD2	LEU- 198	3.62	0	Hydrophobic	false
F61	CB	LEU- 198	4.05	0	Hydrophobic	false
F60	CG	LEU- 198	4.4	0	Hydrophobic	false
C37	CZ	TYR- 199	3.54	0	Hydrophobic	false
F60	CD1	TYR- 199	4.04	0	Hydrophobic	false
F61	CB	TYR- 199	3.7	0	Hydrophobic	false