scPDB - 4qnq entry

Protein Data Bank Entry:

PDB ID : 4qnq

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2014-06-18

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Bcl-2-like protein 1
ID:	B2CL1_RAT
AC:	P53563
Organism:	Rattus norvegicus
Reign:	Eukaryota
TaxID:	10116
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
B	24 %
C	6 %
H	2 %
L	69 %

Ligand binding site composition:

B-Factor:	53.247
Number of residues:	57
Including
Standard Amino Acids:	54
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.325	2241.000

% Hydrophobic	% Polar
43.37	56.63
According to VolSite

Ligand :

HET Code:	1XJ
Formula:	C47H57ClF3N5O6S3
Molecular weight:	976.629 g/mol
DrugBank ID:	DB12340
Buried Surface Area:	61.84 %
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
47.2118	-55.0726	-24.0843

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
N50	OE2	GLU- 96	3.13	0	Ionic (Ligand Cationic)	false
N50	OE1	GLU- 96	3.11	0	Ionic (Ligand Cationic)	false
N50	OE1	GLU- 96	3.11	167.12	H-Bond (Ligand Donor)	false
S62	CG	GLU- 96	3.79	0	Hydrophobic	false
C32	CE1	PHE- 97	4.2	0	Hydrophobic	false
CL6	CE2	PHE- 97	4.3	0	Hydrophobic	false
C3	CB	PHE- 97	3.84	0	Hydrophobic	false
S62	CD	ARG- 100	4.44	0	Hydrophobic	false
C32	CE1	TYR- 101	3.69	0	Hydrophobic	false
CL6	CE1	PHE- 105	3.28	0	Hydrophobic	false
C28	CD2	LEU- 108	3.99	0	Hydrophobic	false
C4	CD2	LEU- 108	3.61	0	Hydrophobic	false
C46	CZ	TYR- 120	4.09	0	Hydrophobic	false
F60	CD2	TYR- 120	4.24	0	Hydrophobic	false
C13	CB	TYR- 120	4.06	0	Hydrophobic	false
F61	CE2	TYR- 120	3.47	0	Hydrophobic	false
C28	CG1	VAL- 126	3.99	0	Hydrophobic	false
C41	CB	GLU- 129	4.47	0	Hydrophobic	false
C31	CD1	LEU- 130	4.46	0	Hydrophobic	false
C40	CD1	LEU- 130	3.9	0	Hydrophobic	false
C16	CB	TRP- 137	4.44	0	Hydrophobic	false
F60	CB	TRP- 137	3.61	0	Hydrophobic	false
O56	N	GLY- 138	3.06	140.68	H-Bond (Protein Donor)	false
C9	CG	ARG- 139	4.2	0	Hydrophobic	false
C3	CG1	VAL- 141	3.81	0	Hydrophobic	false
C5	CB	ALA- 142	4.03	0	Hydrophobic	false
CL6	CB	SER- 145	4	0	Hydrophobic	false
C15	CB	PHE- 146	3.76	0	Hydrophobic	false
DuAr	CZ	ARG- 165	3.65	21.17	Pi/Cation	false
C6	CD	ARG- 165	3.96	0	Hydrophobic	false
C47	CE1	PHE- 191	3.98	0	Hydrophobic	false
F59	CZ	PHE- 191	3.75	0	Hydrophobic	false
F60	CD1	PHE- 191	4.29	0	Hydrophobic	false
F60	CB	LEU- 194	3.72	0	Hydrophobic	false
C38	CZ	TYR- 195	3.66	0	Hydrophobic	false
C43	CE1	TYR- 195	3.69	0	Hydrophobic	false
F59	CB	TYR- 195	3.6	0	Hydrophobic	false
O57	O	HOH- 403	2.5	155.77	H-Bond (Protein Donor)	false
O57	O	HOH- 403	2.91	155.62	H-Bond (Protein Donor)	false