scPDB - 4nbn entry

Protein Data Bank Entry:

PDB ID : 4nbn

Resolution :1.750 Å

Experimental Method : X-ray

Deposition Date : 2013-10-23

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Caspase-6
ID:	CASP6_HUMAN
AC:	P55212
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	3.4.22.59

Chains:

Chain Name:	Percentage of Residues within binding site
A	50 %
B	50 %

Ligand binding site composition:

B-Factor:	18.743
Number of residues:	28
Including
Standard Amino Acids:	26
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.628	432.000

% Hydrophobic	% Polar
62.50	37.50
According to VolSite

Ligand :

HET Code:	2J7
Formula:	C18H18N4O2
Molecular weight:	322.361 g/mol
DrugBank ID:	-
Buried Surface Area:	70.2 %
Polar Surface area:	90.3 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	4
Rings:	3
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
26.2423	28.9997	7.06333

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
C7	CD1	TYR- 198	4.02	0	Hydrophobic	false
C10	CB	TYR- 198	3.77	0	Hydrophobic	false
C4	CB	TYR- 198	4.39	0	Hydrophobic	false
C16	CD1	TYR- 198	4.04	0	Hydrophobic	false
C22	CB	TYR- 198	4.44	0	Hydrophobic	false
C10	CG	TYR- 198	3.47	0	Hydrophobic	false
C3	CG2	THR- 199	4.47	0	Hydrophobic	false
C21	CG2	THR- 199	4.41	0	Hydrophobic	false
O23	N	THR- 199	2.94	166.83	H-Bond (Protein Donor)	false
O24	N	THR- 199	3.02	168.1	H-Bond (Protein Donor)	false
C7	CD2	LEU- 200	3.33	0	Hydrophobic	false
C16	CD2	LEU- 200	3.33	0	Hydrophobic	false
C4	CG	PRO- 201	4.32	0	Hydrophobic	false
C22	CG	PRO- 201	4.32	0	Hydrophobic	false
C6	CG	GLU- 214	3.72	0	Hydrophobic	false
C22	CB	GLU- 214	3.81	0	Hydrophobic	false
C19	CG	GLU- 214	3.68	0	Hydrophobic	false
C20	CB	GLU- 214	3.68	0	Hydrophobic	false
C4	CB	GLU- 214	3.69	0	Hydrophobic	false