scPDB - 1ppm entry

Protein Data Bank Entry:

PDB ID : 1ppm

Resolution :1.700 Å

Experimental Method : X-ray

Deposition Date : 1992-06-01

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	5.570	6.140	6.140	0.580	6.720	2

List of CHEMBLId :

CHEMBL3142426

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:	12.291
Number of residues:	40
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.982	914.625

% Hydrophobic	% Polar
41.33	58.67
According to VolSite

Ligand :

HET Code:	0P1
Formula:	C29H39N3O9P
Molecular weight:	604.608 g/mol
DrugBank ID:	-
Buried Surface Area:	53.21 %
Polar Surface area:	181.99 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	3
Rings:	2
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	17

Mass center Coordinates

X	Y	Z
20.108	8.53524	21.478

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
C8	CG	GLU- 15	4.48	0	Hydrophobic	false
O11	OD1	ASP- 33	2.54	167.31	H-Bond (Protein Donor)	false
CB2	CD2	TYR- 75	3.91	0	Hydrophobic	false
CD2	CB	TYR- 75	3.56	0	Hydrophobic	false
O4	N	GLY- 76	2.93	129.5	H-Bond (Protein Donor)	false
N1	OD1	ASP- 77	2.79	172.13	H-Bond (Ligand Donor)	false
O3	N	ASP- 77	3	136.5	H-Bond (Protein Donor)	false
CB1	CB	ASP- 77	3.74	0	Hydrophobic	false
CD1	CE2	PHE- 112	4.39	0	Hydrophobic	false
CD2	CZ	PHE- 112	4.15	0	Hydrophobic	false
CB2	CD2	LEU- 121	4.36	0	Hydrophobic	false
CD1	CD2	LEU- 121	3.89	0	Hydrophobic	false
CB3	CE1	PHE- 190	4.34	0	Hydrophobic	false
CS	CZ	PHE- 190	4.34	0	Hydrophobic	false
CB3	CD1	ILE- 211	3.88	0	Hydrophobic	false
O21	OD1	ASP- 213	2.65	149.89	H-Bond (Protein Donor)	false
N2	O	GLY- 215	3.19	147.15	H-Bond (Ligand Donor)	false
CB1	CG2	THR- 216	4.36	0	Hydrophobic	false
O21	OG1	THR- 216	3.3	147.64	H-Bond (Protein Donor)	false
C2	CB	THR- 217	3.98	0	Hydrophobic	false
N	OG1	THR- 217	2.94	128.22	H-Bond (Ligand Donor)	false
O	N	THR- 217	2.99	169.98	H-Bond (Protein Donor)	false
C2	CD1	LEU- 218	3.72	0	Hydrophobic	false
C5	CD2	LEU- 284	3.91	0	Hydrophobic	false
CE1	CD1	ILE- 293	3.84	0	Hydrophobic	false
CZ	CD1	ILE- 297	3.95	0	Hydrophobic	false
CE2	CG1	ILE- 297	3.94	0	Hydrophobic	false