scPDB - 3psy entry

Protein Data Bank Entry:

PDB ID : 3psy

Resolution :1.430 Å

Experimental Method : X-ray

Deposition Date : 2010-12-02

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:	14.284
Number of residues:	35
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.341	621.000

% Hydrophobic	% Polar
38.04	61.96
According to VolSite

Ligand :

HET Code:	RB9
Formula:	C30H29N4O2S
Molecular weight:	509.642 g/mol
DrugBank ID:	-
Buried Surface Area:	57.78 %
Polar Surface area:	118.83 Å2

Number of
H-Bond Acceptors:	2
H-Bond Donors:	4
Rings:	5
Aromatic rings:	5
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	10

Mass center Coordinates

X	Y	Z
-1.89073	6.06711	8.97222

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
N3	OD1	ASP- 35	3.38	122.84	H-Bond (Ligand Donor)	false
N3	OD2	ASP- 35	2.58	160.44	H-Bond (Ligand Donor)	false
N3	OD1	ASP- 35	3.38	0	Ionic (Ligand Cationic)	false
N3	OD2	ASP- 35	2.58	0	Ionic (Ligand Cationic)	false
C12	CD2	TYR- 79	3.65	0	Hydrophobic	false
O1	N	GLY- 80	2.76	142.61	H-Bond (Protein Donor)	false
N4	OD2	ASP- 81	2.92	162.47	H-Bond (Ligand Donor)	false
C22	CB	ASP- 81	3.69	0	Hydrophobic	false
C28	CD1	ILE- 122	3.88	0	Hydrophobic	false
C12	CD2	LEU- 125	3.85	0	Hydrophobic	false
C27	CD1	LEU- 125	4.45	0	Hydrophobic	false
S1	CD1	ILE- 217	3.71	0	Hydrophobic	false
N2	OD1	ASP- 219	2.66	159.6	H-Bond (Ligand Donor)	false
N1	OG1	THR- 222	2.79	144.13	H-Bond (Ligand Donor)	false
C19	CG2	THR- 222	3.84	0	Hydrophobic	false
C20	CZ	TYR- 226	3.42	0	Hydrophobic	false
C15	CG1	ILE- 300	3.69	0	Hydrophobic	false
C6	CG2	ILE- 300	3.81	0	Hydrophobic	false
S1	CD1	ILE- 302	3.5	0	Hydrophobic	false
S1	CD1	ILE- 304	4.18	0	Hydrophobic	false
C14	CD1	ILE- 304	4.25	0	Hydrophobic	false