scPDB - 1psa entry

Protein Data Bank Entry:

PDB ID : 1psa

Resolution :2.900 Å

Experimental Method : X-ray

Deposition Date : 1991-10-22

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Pepsin A
ID:	PEPA_PIG
AC:	P00791
Organism:	Sus scrofa
Reign:	Eukaryota
TaxID:	9823
EC Number:	3.4.23.1

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	9.040
Number of residues:	38
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.247	934.875

% Hydrophobic	% Polar
47.29	52.71
According to VolSite

Ligand :

HET Code:	0ZL
Formula:	C29H55N3O6
Molecular weight:	541.763 g/mol
DrugBank ID:	-
Buried Surface Area:	60.09 %
Polar Surface area:	136.98 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	5
Rings:	1
Aromatic rings:	0
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	17

Mass center Coordinates

X	Y	Z
33.2237	5.92116	-0.289921

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
C3	CG2	THR- 12	4.15	0	Hydrophobic	false
CD1	CG	GLU- 13	3.99	0	Hydrophobic	false
CD1	CD1	ILE- 30	4.14	0	Hydrophobic	false
C6'	CG2	ILE- 30	4.13	0	Hydrophobic	false
C5'	CG1	ILE- 30	4.17	0	Hydrophobic	false
O21	OD1	ASP- 32	2.92	162.88	H-Bond (Ligand Donor)	false
C21	CD1	TYR- 75	4.31	0	Hydrophobic	false
C7'	CD1	TYR- 75	4.19	0	Hydrophobic	false
C2'	CB	TYR- 75	3.69	0	Hydrophobic	false
O31	N	GLY- 76	3.4	155.35	H-Bond (Protein Donor)	false
N1	OG1	THR- 77	3.11	163.34	H-Bond (Ligand Donor)	false
O3	N	THR- 77	2.81	148.21	H-Bond (Protein Donor)	false
CB1	CG2	THR- 77	3.91	0	Hydrophobic	false
C3'	CB	THR- 77	4.27	0	Hydrophobic	false
C3'	CE2	PHE- 111	4.35	0	Hydrophobic	false
C5'	CZ	PHE- 117	3.75	0	Hydrophobic	false
C4'	CD1	ILE- 120	3.63	0	Hydrophobic	false
C7	CE1	TYR- 189	3.95	0	Hydrophobic	false
C7	CD1	ILE- 213	3.64	0	Hydrophobic	false
O21	OD2	ASP- 215	2.7	149.77	H-Bond (Protein Donor)	false
N2	O	GLY- 217	2.98	147.57	H-Bond (Ligand Donor)	false
CD11	CG2	THR- 218	3.87	0	Hydrophobic	false
O21	OG1	THR- 218	3.43	143.05	H-Bond (Protein Donor)	false
N	OG	SER- 219	2.81	151.16	H-Bond (Ligand Donor)	false
O	N	SER- 219	3.11	157.91	H-Bond (Protein Donor)	false
C3	CD1	LEU- 220	3.87	0	Hydrophobic	false
CD11	CG2	THR- 222	4.36	0	Hydrophobic	false
CD21	CE	MET- 289	3.54	0	Hydrophobic	false
C7	CG1	VAL- 291	4.32	0	Hydrophobic	false
CD11	CD1	ILE- 300	3.77	0	Hydrophobic	false
C6	CD1	ILE- 300	3.69	0	Hydrophobic	false
O	O	HOH- 347	2.71	157.43	H-Bond (Protein Donor)	false