scPDB - 4x3u entry

Protein Data Bank Entry:

PDB ID : 4x3u

Resolution :1.630 Å

Experimental Method : X-ray

Deposition Date : 2014-12-01

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Chromobox protein homolog 7
ID:	CBX7_MOUSE
AC:	Q8VDS3
Organism:	Mus musculus
Reign:	Eukaryota
TaxID:	10090
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	49 %
B	51 %

Ligand binding site composition:

B-Factor:	16.355
Number of residues:	48
Including
Standard Amino Acids:	45
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.142	742.500

% Hydrophobic	% Polar
66.36	33.64
According to VolSite

Ligand :

HET Code:	SVR
Formula:	C51H34N6O23S6
Molecular weight:	1291.232 g/mol
DrugBank ID:	DB04786
Buried Surface Area:	46.61 %
Polar Surface area:	551 Å2

Number of
H-Bond Acceptors:	23
H-Bond Donors:	6
Rings:	8
Aromatic rings:	8
Anionic atoms:	6
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	16

Mass center Coordinates

X	Y	Z
-0.00997674	-15.624	11.0159

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
O34	NH2	ARG- 20	3.35	138.88	H-Bond (Protein Donor)	false
O34	NH1	ARG- 20	2.97	162.62	H-Bond (Protein Donor)	false
O86	NH1	ARG- 20	2.8	165.32	H-Bond (Protein Donor)	false
O34	CZ	ARG- 20	3.61	0	Ionic (Protein Cationic)	false
O86	CZ	ARG- 20	3.59	0	Ionic (Protein Cationic)	false
O86	CZ	ARG- 22	3.72	0	Ionic (Protein Cationic)	false
O86	NH1	ARG- 22	3.17	124.27	H-Bond (Protein Donor)	false
C12	CD1	LEU- 29	4.4	0	Hydrophobic	false
C70	CD1	LEU- 29	3.99	0	Hydrophobic	false
C40	CB	TRP- 32	4.22	0	Hydrophobic	false
C50	CB	TRP- 32	4.11	0	Hydrophobic	false
C42	CE2	TRP- 32	3.45	0	Hydrophobic	false
C48	CE2	TRP- 32	3.47	0	Hydrophobic	false
C40	CE2	TRP- 35	3.47	0	Hydrophobic	false
C8	CB	TYR- 39	4.31	0	Hydrophobic	false
C27	CD1	TYR- 39	4.03	0	Hydrophobic	false
C56	CB	TYR- 39	4.21	0	Hydrophobic	false
C57	CB	TYR- 39	4.49	0	Hydrophobic	false
C59	CD1	TYR- 39	4.05	0	Hydrophobic	false
N19	O	TYR- 39	2.89	140.62	H-Bond (Ligand Donor)	false
N53	O	TYR- 39	2.98	149.02	H-Bond (Ligand Donor)	false
N1	O	SER- 40	2.77	122.75	H-Bond (Ligand Donor)	false
N63	O	SER- 40	2.56	125.1	H-Bond (Ligand Donor)	false
C8	CG2	THR- 41	3.77	0	Hydrophobic	false
C56	CG2	THR- 41	3.69	0	Hydrophobic	false
C49	CG2	THR- 41	3.63	0	Hydrophobic	false
C33	CG2	THR- 41	3.64	0	Hydrophobic	false
O81	NE1	TRP- 42	2.95	156.98	H-Bond (Protein Donor)	false
O79	N	TRP- 42	3.14	160.56	H-Bond (Protein Donor)	false
O23	NE2	HIS- 47	2.76	144.03	H-Bond (Protein Donor)	false
O24	NE2	HIS- 47	3.25	147.92	H-Bond (Protein Donor)	false
O77	NE2	HIS- 47	2.65	160.38	H-Bond (Protein Donor)	false
C14	CD1	LEU- 49	4.33	0	Hydrophobic	false
C27	CD1	LEU- 49	3.92	0	Hydrophobic	false
C59	CD2	LEU- 49	3.98	0	Hydrophobic	false
N44	O	HOH- 131	2.89	152.89	H-Bond (Ligand Donor)	false