scPDB - 1bxo entry

Protein Data Bank Entry:

PDB ID : 1bxo

Resolution :0.950 Å

Experimental Method : X-ray

Deposition Date : 1998-10-07

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	7.000	7.000	7.000	0.000	7.000	1

List of CHEMBLId :

CHEMBL315745

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:	12.038
Number of residues:	40
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.753	762.750

% Hydrophobic	% Polar
40.27	59.73
According to VolSite

Ligand :

HET Code:	PP7
Formula:	C30H46N4O9P
Molecular weight:	637.681 g/mol
DrugBank ID:	-
Buried Surface Area:	58.37 %
Polar Surface area:	201.86 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	4
Rings:	2
Aromatic rings:	1
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	10

Mass center Coordinates

X	Y	Z
20.8895	9.12439	21.6976

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
CV1	CG	GLU- 15	3.83	0	Hydrophobic	false
CV9	CG	GLU- 16	4.16	0	Hydrophobic	false
O3	OD1	ASP- 33	3.17	167.65	H-Bond (Ligand Donor)	false
CBL	CD1	TYR- 75	3.92	0	Hydrophobic	false
CL2	CG	TYR- 75	3.63	0	Hydrophobic	false
OT2	N	GLY- 76	2.93	128.87	H-Bond (Protein Donor)	false
N1	OD2	ASP- 77	2.89	159.94	H-Bond (Ligand Donor)	false
C2	CB	ASP- 77	3.79	0	Hydrophobic	false
O1	N	ASP- 77	3.14	145.88	H-Bond (Protein Donor)	false
CL2	CZ	PHE- 112	4.26	0	Hydrophobic	false
CBL	CD2	LEU- 121	4.22	0	Hydrophobic	false
CL1	CD2	LEU- 121	3.89	0	Hydrophobic	false
C6	CE1	PHE- 190	4.16	0	Hydrophobic	false
C7	CZ	PHE- 190	4.29	0	Hydrophobic	false
C6	CD1	ILE- 211	3.87	0	Hydrophobic	false
NL	O	GLY- 215	3.06	144.29	H-Bond (Ligand Donor)	false
N2	OG1	THR- 216	3.01	158.54	H-Bond (Ligand Donor)	false
NV2	OG1	THR- 217	2.94	173.59	H-Bond (Ligand Donor)	false
CV1	CB	THR- 217	4.05	0	Hydrophobic	false
CV3	CB	THR- 217	4.41	0	Hydrophobic	false
CV4	CG2	THR- 217	4.47	0	Hydrophobic	false
OV2	N	THR- 217	3.05	168.74	H-Bond (Protein Donor)	false
CV3	CD1	LEU- 218	3.8	0	Hydrophobic	false
CV4	CE2	TYR- 274	3.85	0	Hydrophobic	false
CV4	CD2	LEU- 284	3.93	0	Hydrophobic	false
CD1	CD1	ILE- 293	3.87	0	Hydrophobic	false
CD1	CD1	ILE- 297	3.53	0	Hydrophobic	false