scPDB - 1gvt entry

Protein Data Bank Entry:

PDB ID : 1gvt

Resolution :0.980 Å

Experimental Method : X-ray

Deposition Date : 2002-02-27

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:	7.228
Number of residues:	36
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.637	759.375

% Hydrophobic	% Polar
38.67	61.33
According to VolSite

Ligand :

HET Code:	2ZS
Formula:	C31H48N4O7S
Molecular weight:	620.800 g/mol
DrugBank ID:	-
Buried Surface Area:	60.49 %
Polar Surface area:	171.6 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	4
Rings:	3
Aromatic rings:	1
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	15

Mass center Coordinates

X	Y	Z
3.82881	269.04	17.007

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
CE2	CD1	ILE- 10	4.09	0	Hydrophobic	false
CE2	CB	ASP- 15	3.57	0	Hydrophobic	false
CD2	CB	ALA- 16	4.36	0	Hydrophobic	false
CE11	CB	ASP- 33	4.49	0	Hydrophobic	false
OH	OD1	ASP- 35	2.63	168.84	H-Bond (Ligand Donor)	false
OH	OD2	ASP- 35	3.33	126.38	H-Bond (Ligand Donor)	false
CB2	CD1	TYR- 79	4.08	0	Hydrophobic	false
CD21	CG	TYR- 79	3.69	0	Hydrophobic	false
CH	CD1	TYR- 79	3.98	0	Hydrophobic	false
O11	N	GLY- 80	2.94	161.59	H-Bond (Protein Donor)	false
N1	OD2	ASP- 81	2.94	174.2	H-Bond (Ligand Donor)	false
CB1	CB	ASP- 81	3.81	0	Hydrophobic	false
O3	N	ASP- 81	3.02	140.9	H-Bond (Protein Donor)	false
CE21	CZ	PHE- 116	3.94	0	Hydrophobic	false
CZ1	CE1	PHE- 116	3.59	0	Hydrophobic	false
CE11	CD1	ILE- 122	4.33	0	Hydrophobic	false
CE1	CD1	ILE- 122	4.28	0	Hydrophobic	false
CD11	CD2	LEU- 125	3.89	0	Hydrophobic	false
CZ1	CD1	LEU- 125	4.28	0	Hydrophobic	false
CM1	CE1	PHE- 194	3.57	0	Hydrophobic	false
CM1	CD1	ILE- 217	4.4	0	Hydrophobic	false
CM2	CD1	ILE- 217	4.17	0	Hydrophobic	false
OH	OD2	ASP- 219	2.65	151.27	H-Bond (Protein Donor)	false
O21	OD2	ASP- 219	2.93	127.35	H-Bond (Protein Donor)	false
N2	O	GLY- 221	3.03	140.29	H-Bond (Ligand Donor)	false
SG	CG2	THR- 222	4.41	0	Hydrophobic	false
C2	CG2	THR- 223	3.83	0	Hydrophobic	false
C3	CB	THR- 223	3.85	0	Hydrophobic	false
O2	N	THR- 223	3.02	161.78	H-Bond (Protein Donor)	false
C2	CG	LEU- 224	3.92	0	Hydrophobic	false
C6	CD1	LEU- 224	3.71	0	Hydrophobic	false
C2	CZ	PHE- 280	3.67	0	Hydrophobic	false
C6	CE2	PHE- 291	4.12	0	Hydrophobic	false
CS	CD1	ILE- 300	3.44	0	Hydrophobic	false
CM2	CD1	ILE- 304	3.46	0	Hydrophobic	false
CS	CD1	ILE- 304	3.9	0	Hydrophobic	false