scPDB - 1gvw entry

Protein Data Bank Entry:

PDB ID : 1gvw

Resolution :1.000 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:	14.461
Number of residues:	43
Including
Standard Amino Acids:	41
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.712	789.750

% Hydrophobic	% Polar
41.88	58.12
According to VolSite

Ligand :

HET Code:	0EM
Formula:	C32H50N6O7P
Molecular weight:	661.749 g/mol
DrugBank ID:	-
Buried Surface Area:	53.53 %
Polar Surface area:	204.24 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	5
Rings:	2
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	19

Mass center Coordinates

X	Y	Z
3.56226	31.256	16.656

Binding mode :

What is Poseview ?

2D View
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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
CZ	CD1	ILE- 10	3.92	0	Hydrophobic	false
CE1	CB	ASP- 15	3.71	0	Hydrophobic	false
CZ	CB	ALA- 16	4.28	0	Hydrophobic	false
N3	O	GLY- 37	3.08	158.4	H-Bond (Ligand Donor)	false
CB3	CB	SER- 38	4.28	0	Hydrophobic	false
CG11	CG1	ILE- 77	4.24	0	Hydrophobic	false
CD12	CD1	ILE- 77	4.21	0	Hydrophobic	false
CB2	CD1	TYR- 79	3.95	0	Hydrophobic	false
CD22	CB	TYR- 79	3.56	0	Hydrophobic	false
O4	N	GLY- 80	2.83	148.1	H-Bond (Protein Donor)	false
N1	OD2	ASP- 81	3.08	176.01	H-Bond (Ligand Donor)	false
O3	N	ASP- 81	3.13	139.55	H-Bond (Protein Donor)	false
CB1	CB	ASP- 81	3.89	0	Hydrophobic	false
CD22	CZ	PHE- 116	4.48	0	Hydrophobic	false
CE2	CD1	ILE- 122	3.77	0	Hydrophobic	false
CB2	CD2	LEU- 125	4.42	0	Hydrophobic	false
CD11	CD2	LEU- 125	3.94	0	Hydrophobic	false
CD12	CB	LEU- 133	4.33	0	Hydrophobic	false
CG21	CZ	PHE- 194	3.81	0	Hydrophobic	false
O1P	OD1	ASP- 219	2.58	155	H-Bond (Protein Donor)	false
N2	O	GLY- 221	3.28	137.2	H-Bond (Ligand Donor)	false
O1P	OG1	THR- 222	3.34	155.71	H-Bond (Protein Donor)	false
N	OG1	THR- 223	2.83	141.64	H-Bond (Ligand Donor)	false
O	N	THR- 223	3.09	164.97	H-Bond (Protein Donor)	false
C2	CD1	LEU- 224	4.16	0	Hydrophobic	false
C3	CD1	LEU- 224	3.97	0	Hydrophobic	false
C2	CE2	PHE- 280	3.33	0	Hydrophobic	false