scPDB - 1nmq entry

Protein Data Bank Entry:

PDB ID : 1nmq

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 2003-01-10

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Caspase-3
ID:	CASP3_HUMAN
AC:	P42574
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	3.4.22.56

Chains:

Chain Name:	Percentage of Residues within binding site
A	3 %
B	97 %

Ligand binding site composition:

B-Factor:	24.621
Number of residues:	34
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.095	388.125

% Hydrophobic	% Polar
33.04	66.96
According to VolSite

Ligand :

HET Code:	160
Formula:	C20H23N2O8S5
Molecular weight:	579.730 g/mol
DrugBank ID:	-
Buried Surface Area:	57.97 %
Polar Surface area:	262.21 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	2
Rings:	2
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	14

Mass center Coordinates

X	Y	Z
5.91906	33.3629	33.534

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
O31	NE	ARG- 64	2.69	157.22	H-Bond (Protein Donor)	false
O32	NH2	ARG- 64	2.56	173.75	H-Bond (Protein Donor)	false
O32	NE	ARG- 64	3.31	129.07	H-Bond (Protein Donor)	false
O31	CZ	ARG- 64	3.51	0	Ionic (Protein Cationic)	false
O32	CZ	ARG- 64	3.36	0	Ionic (Protein Cationic)	false
O26	N	GLY- 122	3.14	152.33	H-Bond (Protein Donor)	false
O32	NE2	GLN- 161	2.86	160.56	H-Bond (Protein Donor)	false
C1	CD2	TYR- 204	4.2	0	Hydrophobic	false
C8	CE2	TYR- 204	3.49	0	Hydrophobic	false
N4	O	SER- 205	3.03	138.41	H-Bond (Ligand Donor)	false
C29	CB	SER- 205	4.48	0	Hydrophobic	false
O28	NH1	ARG- 207	2.76	124.17	H-Bond (Protein Donor)	false
O31	NE	ARG- 207	2.8	145.14	H-Bond (Protein Donor)	false
O31	NH1	ARG- 207	3.1	130.44	H-Bond (Protein Donor)	false
O32	NE	ARG- 207	3.33	146.11	H-Bond (Protein Donor)	false
O31	CZ	ARG- 207	3.35	0	Ionic (Protein Cationic)	false
O34	NE1	TRP- 214	3.21	142.36	H-Bond (Protein Donor)	false
O33	N	PHE- 250	3.07	141.06	H-Bond (Protein Donor)	false
S14	CE1	PHE- 256	3.8	0	Hydrophobic	false
C12	CE2	PHE- 256	4.33	0	Hydrophobic	false