scPDB - 3wiz entry

Protein Data Bank Entry:

PDB ID : 3wiz

Resolution :2.450 Å

Experimental Method : X-ray

Deposition Date : 2013-09-26

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_HUMAN
AC:	Q07817
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	87 %
B	13 %

Ligand binding site composition:

B-Factor:	65.360
Number of residues:	31
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.073	246.375

% Hydrophobic	% Polar
57.53	42.47
According to VolSite

Ligand :

HET Code:	LC6
Formula:	C47H46N6O8S2
Molecular weight:	887.034 g/mol
DrugBank ID:	-
Buried Surface Area:	42.78 %
Polar Surface area:	225.86 Å2

Number of
H-Bond Acceptors:	11
H-Bond Donors:	3
Rings:	7
Aromatic rings:	7
Anionic atoms:	2
Cationic atoms:	2
Rule of Five Violation:	3
Rotatable Bonds:	19

Mass center Coordinates

X	Y	Z
37.0914	11.9303	-46.6775

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
N52	OE1	GLU- 96	3.08	128.83	H-Bond (Ligand Donor)	false
N52	OE1	GLU- 96	3.08	0	Ionic (Ligand Cationic)	false
S62	CG	GLU- 96	3.89	0	Hydrophobic	false
C38	CE1	PHE- 97	4.34	0	Hydrophobic	false
C1	CD1	PHE- 97	3.49	0	Hydrophobic	false
C15	CB	PHE- 97	4.03	0	Hydrophobic	false
S62	CD	ARG- 100	4.29	0	Hydrophobic	false
C9	CD2	LEU- 108	3.71	0	Hydrophobic	false
C2	CG1	VAL- 126	3.9	0	Hydrophobic	false
C27	CB	GLU- 129	3.61	0	Hydrophobic	false
C20	CB	GLU- 129	3.74	0	Hydrophobic	false
C38	CD1	LEU- 130	4.4	0	Hydrophobic	false
C42	CD1	LEU- 130	4.46	0	Hydrophobic	false
C8	CB	LEU- 130	3.89	0	Hydrophobic	false
O58	N	GLY- 138	3.28	132.24	H-Bond (Protein Donor)	false
C38	CG	ARG- 139	4.04	0	Hydrophobic	false
O60	NH2	ARG- 139	2.97	135.27	H-Bond (Protein Donor)	false
O60	NE	ARG- 139	2.71	151.14	H-Bond (Protein Donor)	false
O60	CZ	ARG- 139	3.25	0	Ionic (Protein Cationic)	false
C5	CG1	VAL- 141	3.8	0	Hydrophobic	false
C38	CB	ALA- 142	3.95	0	Hydrophobic	false
C47	CD1	TYR- 195	4.29	0	Hydrophobic	false