scPDB - 1qrp entry

Protein Data Bank Entry:

PDB ID : 1qrp

Resolution :1.960 Å

Experimental Method : X-ray

Deposition Date : 1999-06-15

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Pepsin A-4
ID:	PEPA4_HUMAN
AC:	P0DJD7
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	3.4.23.1

Chains:

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

Ligand binding site composition:

B-Factor:	21.068
Number of residues:	46
Including
Standard Amino Acids:	43
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.150	688.500

% Hydrophobic	% Polar
43.14	56.86
According to VolSite

Ligand :

HET Code:	HH0
Formula:	C36H59N5O10P
Molecular weight:	752.855 g/mol
DrugBank ID:	-
Buried Surface Area:	52.31 %
Polar Surface area:	230.96 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	5
Rings:	1
Aromatic rings:	1
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	22

Mass center Coordinates

X	Y	Z
7.30717	17.6227	10.1816

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
CW1	CE	MET- 12	3.8	0	Hydrophobic	false
CZ2	CE	MET- 12	3.41	0	Hydrophobic	false
CG1	CG	GLU- 13	3.62	0	Hydrophobic	false
CN1	CG1	VAL- 30	3.97	0	Hydrophobic	false
N6	O	GLY- 34	3.05	172.54	H-Bond (Ligand Donor)	false
CB6	CB	SER- 35	3.59	0	Hydrophobic	false
CB6	CG2	ILE- 73	4.24	0	Hydrophobic	false
N7	O	THR- 74	2.99	157.11	H-Bond (Ligand Donor)	false
CB7	CB	THR- 74	4.46	0	Hydrophobic	false
CB4	CD1	TYR- 75	4.35	0	Hydrophobic	false
CM2	CG	TYR- 75	4.09	0	Hydrophobic	false
CB6	CD1	TYR- 75	4.2	0	Hydrophobic	false
O5	N	GLY- 76	3.08	138.33	H-Bond (Protein Donor)	false
N3	OG1	THR- 77	3	162.27	H-Bond (Ligand Donor)	false
O3	N	THR- 77	2.93	144.54	H-Bond (Protein Donor)	false
CB3	CG2	THR- 77	4.29	0	Hydrophobic	false
CM2	CE2	PHE- 111	4.28	0	Hydrophobic	false
CG1	CZ	PHE- 111	3.55	0	Hydrophobic	false
CN1	CZ	PHE- 117	3.98	0	Hydrophobic	false
CM2	CD1	ILE- 120	3.78	0	Hydrophobic	false
O6	OH	TYR- 189	2.74	174.42	H-Bond (Protein Donor)	false
CV1	CZ	TYR- 189	3.26	0	Hydrophobic	false
CU1	CD1	ILE- 213	3.51	0	Hydrophobic	false
O11	OD2	ASP- 215	2.76	135.66	H-Bond (Protein Donor)	false
N5	O	GLY- 217	3.06	151.71	H-Bond (Ligand Donor)	false
CO2	CG2	THR- 218	4.44	0	Hydrophobic	false
O11	OG1	THR- 218	3.23	150.52	H-Bond (Protein Donor)	false
CA1	CB	SER- 219	3.96	0	Hydrophobic	false
CG2	CB	SER- 219	4.28	0	Hydrophobic	false
N1	OG	SER- 219	3.06	124.44	H-Bond (Ligand Donor)	false
O2	N	SER- 219	2.96	164.34	H-Bond (Protein Donor)	false
CW1	CD1	LEU- 220	4.17	0	Hydrophobic	false
CO2	SD	MET- 289	4.14	0	Hydrophobic	false
CP1	SD	MET- 289	4.21	0	Hydrophobic	false
CE2	CD2	LEU- 291	3.72	0	Hydrophobic	false
CV1	CD1	LEU- 298	3.72	0	Hydrophobic	false
CP1	CD1	ILE- 300	4.36	0	Hydrophobic	false
CB5	CD1	ILE- 300	3.89	0	Hydrophobic	false
O2	O	HOH- 461	2.8	179.96	H-Bond (Protein Donor)	false