scPDB - 1ppk entry

Protein Data Bank Entry:

PDB ID : 1ppk

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 1994-01-20

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	4.700	4.700	4.700	0.000	4.700	1

List of CHEMBLId :

CHEMBL82364

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
E	100 %

Ligand binding site composition:

B-Factor:	10.578
Number of residues:	37
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.313	634.500

% Hydrophobic	% Polar
38.30	61.70
According to VolSite

Ligand :

HET Code:	IVV
Formula:	C24H45N3O7P
Molecular weight:	518.604 g/mol
DrugBank ID:	-
Buried Surface Area:	55.25 %
Polar Surface area:	163.53 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	3
Rings:	0
Aromatic rings:	0
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	16

Mass center Coordinates

X	Y	Z
20.7029	8.21331	20.8242

Binding mode :

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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
CA1	CG	GLU- 15	3.62	0	Hydrophobic	false
C7	CB	SER- 36	3.74	0	Hydrophobic	false
CB4	CD2	TYR- 75	4.08	0	Hydrophobic	false
CD2	CG	TYR- 75	3.53	0	Hydrophobic	false
O4	N	GLY- 76	2.82	155.83	H-Bond (Protein Donor)	false
N3	OD1	ASP- 77	2.88	175.27	H-Bond (Ligand Donor)	false
O3	N	ASP- 77	3.09	133.23	H-Bond (Protein Donor)	false
CB3	CB	ASP- 77	3.84	0	Hydrophobic	false
CD2	CZ	PHE- 112	4.17	0	Hydrophobic	false
CB4	CD2	LEU- 121	4.33	0	Hydrophobic	false
CD1	CD2	LEU- 121	4	0	Hydrophobic	false
C7	CE1	PHE- 190	4.03	0	Hydrophobic	false
O1P	OD1	ASP- 213	2.56	151.69	H-Bond (Protein Donor)	false
N4	O	GLY- 215	3.15	142.25	H-Bond (Ligand Donor)	false
CG13	CG2	THR- 216	4.4	0	Hydrophobic	false
O1P	OG1	THR- 216	3.3	153.62	H-Bond (Protein Donor)	false
CA1	CB	THR- 217	3.79	0	Hydrophobic	false
CG21	CB	THR- 217	4.24	0	Hydrophobic	false
N1	OG1	THR- 217	2.81	158	H-Bond (Ligand Donor)	false
O2	N	THR- 217	3.07	169.37	H-Bond (Protein Donor)	false
CG21	CD1	LEU- 218	3.59	0	Hydrophobic	false
CG13	CD1	LEU- 220	4.16	0	Hydrophobic	false
CG23	CD1	LEU- 220	3.97	0	Hydrophobic	false
CG11	CE2	TYR- 274	3.75	0	Hydrophobic	false
CG11	CD2	LEU- 284	3.95	0	Hydrophobic	false
CG13	CD1	ILE- 297	4.23	0	Hydrophobic	false