scPDB - 1od1 entry

Protein Data Bank Entry:

PDB ID : 1od1

Resolution :1.370 Å

Experimental Method : X-ray

Deposition Date : 2003-02-12

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:	15.388
Number of residues:	49
Including
Standard Amino Acids:	45
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.715	793.125

% Hydrophobic	% Polar
39.15	60.85
According to VolSite

Ligand :

HET Code:	0QS
Formula:	C36H56F2N7O8S
Molecular weight:	784.934 g/mol
DrugBank ID:	-
Buried Surface Area:	53.57 %
Polar Surface area:	224.65 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	8
Rings:	4
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	19

Mass center Coordinates

X	Y	Z
35.923	42.7937	1.37396

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
CE2	CD1	ILE- 10	3.9	0	Hydrophobic	false
CE2	CB	ASP- 15	3.9	0	Hydrophobic	false
CD2	CB	ALA- 16	3.94	0	Hydrophobic	false
OH1	OD1	ASP- 35	2.87	162.89	H-Bond (Ligand Donor)	false
N2'	O	GLY- 37	2.88	135.32	H-Bond (Ligand Donor)	false
C61	CD1	ILE- 77	4.27	0	Hydrophobic	false
CD11	CG	TYR- 79	3.6	0	Hydrophobic	false
CH	CD1	TYR- 79	4.25	0	Hydrophobic	false
CB2	CD1	TYR- 79	3.89	0	Hydrophobic	false
O2	N	GLY- 80	2.89	156.21	H-Bond (Protein Donor)	false
N	OD2	ASP- 81	3.03	166.06	H-Bond (Ligand Donor)	false
O1	N	ASP- 81	3.21	135.09	H-Bond (Protein Donor)	false
CB1	CB	ASP- 81	3.98	0	Hydrophobic	false
CE12	CZ	PHE- 116	4.05	0	Hydrophobic	false
CZ1	CE1	PHE- 116	3.6	0	Hydrophobic	false
CZ	CD1	ILE- 122	4.16	0	Hydrophobic	false
CD22	CD2	LEU- 125	3.78	0	Hydrophobic	false
CE21	CD1	LEU- 125	4.34	0	Hydrophobic	false
C61	CB	LEU- 133	4.43	0	Hydrophobic	false
C61	CG2	THR- 135	3.87	0	Hydrophobic	false
OH1	OD2	ASP- 219	2.67	151.4	H-Bond (Protein Donor)	false
N1	O	GLY- 221	3.26	138.39	H-Bond (Ligand Donor)	false
CB1	CG2	THR- 222	4.38	0	Hydrophobic	false
N1	OG1	THR- 222	3.41	126.46	H-Bond (Ligand Donor)	false
C2	CB	THR- 223	3.78	0	Hydrophobic	false
N3	OG1	THR- 223	3.21	149.11	H-Bond (Ligand Donor)	false
O	N	THR- 223	3.07	165.73	H-Bond (Protein Donor)	false
C2	CG	LEU- 224	3.94	0	Hydrophobic	false
O	O	HOH- 2416	2.77	157.07	H-Bond (Protein Donor)	false