scPDB - 2wed entry

Protein Data Bank Entry:

PDB ID : 2wed

Resolution :1.500 Å

Experimental Method : X-ray

Deposition Date : 1998-02-03

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Penicillopepsin-1
ID:	PENP_PENJA
AC:	P00798
Organism:	Penicillium janthinellum
Reign:	Eukaryota
TaxID:	5079
EC Number:	3.4.23.20

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	14.870
Number of residues:	33
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.968	880.875

% Hydrophobic	% Polar
39.46	60.54
According to VolSite

Ligand :

HET Code:	PP6
Formula:	C29H32N2O7P
Molecular weight:	551.547 g/mol
DrugBank ID:	-
Buried Surface Area:	47.54 %
Polar Surface area:	143.66 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	2
Rings:	4
Aromatic rings:	3
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
22.39	9.22408	22.4248

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
O	OD2	ASP- 33	2.52	169.71	H-Bond (Protein Donor)	false
C13	CD1	TYR- 75	4	0	Hydrophobic	false
CS	CD1	TYR- 75	4.02	0	Hydrophobic	false
C9	CG	TYR- 75	3.48	0	Hydrophobic	false
OE	N	GLY- 76	2.79	149.12	H-Bond (Protein Donor)	false
OV	N	ASP- 77	3.23	135.9	H-Bond (Protein Donor)	false
CBV	CB	ASP- 77	3.97	0	Hydrophobic	false
C9	CD2	LEU- 121	4.28	0	Hydrophobic	false
C13	CD2	LEU- 121	4.44	0	Hydrophobic	false
CB	CE1	PHE- 190	3.83	0	Hydrophobic	false
OH	OD1	ASP- 213	2.69	145.5	H-Bond (Protein Donor)	false
NL	OG1	THR- 216	3.24	151.36	H-Bond (Ligand Donor)	false
OH	OG1	THR- 216	3.14	151.15	H-Bond (Protein Donor)	false
OI	N	THR- 217	3.03	160.5	H-Bond (Protein Donor)	false
CV1	CD1	LEU- 220	4.15	0	Hydrophobic	false
CV2	CD1	LEU- 220	4.26	0	Hydrophobic	false
CE2	CD1	ILE- 293	4.15	0	Hydrophobic	false
CE1	CD1	ILE- 297	3.89	0	Hydrophobic	false
CZ	CD1	ILE- 297	4.04	0	Hydrophobic	false