scPDB - 1gvv entry

Protein Data Bank Entry:

PDB ID : 1gvv

Resolution :1.050 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:	7.195
Number of residues:	36
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.767	718.875

% Hydrophobic	% Polar
45.07	54.93
According to VolSite

Ligand :

HET Code:	0GM
Formula:	C51H61N5O6
Molecular weight:	840.060 g/mol
DrugBank ID:	-
Buried Surface Area:	54.04 %
Polar Surface area:	165.72 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	6
Rings:	6
Aromatic rings:	5
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	4
Rotatable Bonds:	10

Mass center Coordinates

X	Y	Z
2.02646	273.617	14.1544

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
OH	OD1	ASP- 35	2.51	155.23	H-Bond (Ligand Donor)	false
OH	OD2	ASP- 35	3.18	131.41	H-Bond (Ligand Donor)	false
N2	O	GLY- 37	2.94	169.12	H-Bond (Ligand Donor)	false
CB4	CB	SER- 38	4.09	0	Hydrophobic	false
CD3	CG1	ILE- 77	3.5	0	Hydrophobic	false
N3	O	SER- 78	3.2	155.83	H-Bond (Ligand Donor)	false
CD2	CG	TYR- 79	3.44	0	Hydrophobic	false
CH	CD1	TYR- 79	4.08	0	Hydrophobic	false
CB3	CD1	TYR- 79	3.95	0	Hydrophobic	false
O2	N	GLY- 80	2.79	157.8	H-Bond (Protein Donor)	false
N	OD2	ASP- 81	2.93	154	H-Bond (Ligand Donor)	false
N	OD2	ASP- 81	2.93	0	Ionic (Ligand Cationic)	false
O1	N	ASP- 81	3.12	148.8	H-Bond (Protein Donor)	false
CB	CB	ASP- 81	4.18	0	Hydrophobic	false
CD2	CZ	PHE- 116	4.28	0	Hydrophobic	false
CD1	CD2	LEU- 125	3.91	0	Hydrophobic	false
CD4	CB	LEU- 133	3.9	0	Hydrophobic	false
CB4	CE1	PHE- 194	4.48	0	Hydrophobic	false
OH	OD2	ASP- 219	2.62	153.07	H-Bond (Protein Donor)	false
N1	O	GLY- 221	3.11	137.79	H-Bond (Ligand Donor)	false
CG	CG2	THR- 222	4.4	0	Hydrophobic	false
CZ	CB	ILE- 300	4.45	0	Hydrophobic	false
CG	CD1	ILE- 304	3.98	0	Hydrophobic	false