scPDB - 3prs entry

Protein Data Bank Entry:

PDB ID : 3prs

Resolution :1.380 Å

Experimental Method : X-ray

Deposition Date : 2010-11-30

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Endothiapepsin
ID:	CARP_CRYPA
AC:	P11838
Organism:	Cryphonectria parasitica
Reign:	Eukaryota
TaxID:	5116
EC Number:	3.4.23.22

Chains:

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

Ligand binding site composition:

B-Factor:	10.086
Number of residues:	44
Including
Standard Amino Acids:	42
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.708	725.625

% Hydrophobic	% Polar
43.26	56.74
According to VolSite

Ligand :

HET Code:	RIT
Formula:	C37H48N6O5S2
Molecular weight:	720.944 g/mol
DrugBank ID:	DB00503
Buried Surface Area:	57.43 %
Polar Surface area:	202.26 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	4
Rings:	4
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	18

Mass center Coordinates

X	Y	Z
-1.5608	4.3859	9.18898

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
S81	CD1	ILE- 10	4.14	0	Hydrophobic	false
C86	CD1	ILE- 10	4.48	0	Hydrophobic	false
C90	CD1	ILE- 10	3.94	0	Hydrophobic	false
S81	CB	ASP- 15	4.09	0	Hydrophobic	false
C86	CB	ASP- 15	3.71	0	Hydrophobic	false
S81	CB	ALA- 16	3.98	0	Hydrophobic	false
N11	O	GLY- 37	3.03	146.22	H-Bond (Ligand Donor)	false
S3	CB	SER- 38	4.27	0	Hydrophobic	false
S3	CD1	ILE- 77	4.27	0	Hydrophobic	false
C6	CD2	TYR- 79	4.36	0	Hydrophobic	false
C14	CD2	TYR- 79	4.01	0	Hydrophobic	false
C44	CG	TYR- 79	3.46	0	Hydrophobic	false
O24	N	GLY- 80	2.85	139.1	H-Bond (Protein Donor)	false
N20	OD2	ASP- 81	3.26	158.57	H-Bond (Ligand Donor)	false
O61	N	ASP- 81	2.93	127.96	H-Bond (Protein Donor)	false
C62	CB	ASP- 81	4.05	0	Hydrophobic	false
C90	CB	ASP- 119	4.02	0	Hydrophobic	false
C50	CD1	ILE- 122	4.36	0	Hydrophobic	false
C51	CD2	LEU- 125	3.89	0	Hydrophobic	false
C52	CD1	LEU- 125	4.02	0	Hydrophobic	false
S3	CD1	LEU- 133	4.2	0	Hydrophobic	false
C35	CD1	ILE- 217	3.92	0	Hydrophobic	false
O41	OD2	ASP- 219	2.6	145.42	H-Bond (Ligand Donor)	false
O41	OD1	ASP- 219	3.22	149	H-Bond (Ligand Donor)	false
N58	O	GLY- 221	3.37	154.1	H-Bond (Ligand Donor)	false
C68	CG2	THR- 222	4.08	0	Hydrophobic	false
O76	N	THR- 223	3.24	163.48	H-Bond (Protein Donor)	false
C68	CZ	TYR- 226	3.79	0	Hydrophobic	false
C32	CG2	ILE- 300	3.88	0	Hydrophobic	false
C33	CG2	ILE- 302	4.13	0	Hydrophobic	false
C64	CD1	ILE- 304	3.9	0	Hydrophobic	false
C31	CD1	ILE- 304	3.83	0	Hydrophobic	false
O76	O	HOH- 7002	2.8	135.19	H-Bond (Protein Donor)	false