scPDB - 2pj4 entry

Protein Data Bank Entry:

PDB ID : 2pj4

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2007-04-15

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Carboxypeptidase B
ID:	CBPB1_PIG
AC:	P09955
Organism:	Sus scrofa
Reign:	Eukaryota
TaxID:	9823
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	90 %
B	10 %

Ligand binding site composition:

B-Factor:	14.271
Number of residues:	47
Including
Standard Amino Acids:	40
Non Standard Amino Acids:	1
Water Molecules:	6
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
0.861	1539.000

% Hydrophobic	% Polar
36.40	63.60
According to VolSite

Ligand :

HET Code:	414
Formula:	C24H30N4O7P
Molecular weight:	517.491 g/mol
DrugBank ID:	-
Buried Surface Area:	63.66 %
Polar Surface area:	201.27 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	12

Mass center Coordinates

X	Y	Z
12.3986	23.7778	52.8073

Binding mode :

What is Poseview ?

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3D View

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
O31	NH2	ARG- 71	3	136.93	H-Bond (Protein Donor)	false
C53	CB	TYR- 92	3.92	0	Hydrophobic	false
O35	NH1	ARG- 127	2.89	163.18	H-Bond (Protein Donor)	false
O13	NH2	ARG- 127	3.17	157.03	H-Bond (Protein Donor)	false
O35	CZ	ARG- 127	3.76	0	Ionic (Protein Cationic)	false
O14	ND2	ASN- 144	2.76	168.85	H-Bond (Protein Donor)	false
O14	NH1	ARG- 145	3.02	172.55	H-Bond (Protein Donor)	false
O13	NH2	ARG- 145	2.9	169.09	H-Bond (Protein Donor)	false
O14	CZ	ARG- 145	3.93	0	Ionic (Protein Cationic)	false
O13	CZ	ARG- 145	3.65	0	Ionic (Protein Cationic)	false
C37	CB	GLU- 163	3.84	0	Hydrophobic	false
C40	CG2	THR- 164	3.55	0	Hydrophobic	false
C54	CZ	TYR- 198	3.7	0	Hydrophobic	false
C55	CE1	TYR- 198	4.17	0	Hydrophobic	false
C52	CB	SER- 199	4.21	0	Hydrophobic	false
C5	CG	LEU- 203	3.76	0	Hydrophobic	false
C52	CG2	ILE- 247	4.03	0	Hydrophobic	false
C5	CG1	ILE- 247	3.77	0	Hydrophobic	false
N29	OH	TYR- 248	3	152.47	H-Bond (Ligand Donor)	false
C51	CZ	TYR- 248	4.48	0	Hydrophobic	false
O13	OH	TYR- 248	2.62	175.14	H-Bond (Protein Donor)	false
N12	O	ALA- 250	3.3	156.07	H-Bond (Ligand Donor)	false
N9	OD1	ASP- 255	3.5	126.11	H-Bond (Ligand Donor)	false
N9	OD2	ASP- 255	3.03	171.85	H-Bond (Ligand Donor)	false
N11	OD1	ASP- 255	2.7	157.4	H-Bond (Ligand Donor)	false
C10	OD1	ASP- 255	3.52	0	Ionic (Ligand Cationic)	false
C10	OD2	ASP- 255	3.79	0	Ionic (Ligand Cationic)	false
C5	CG2	THR- 268	3.95	0	Hydrophobic	false
O34	OE2	GLU- 270	2.51	167.61	H-Bond (Protein Donor)	false
O23	OE2	GLU- 270	3.23	121.44	H-Bond (Protein Donor)	false
C55	CZ	PHE- 279	4.17	0	Hydrophobic	false
O34	ZN	ZN- 400	2.68	0	Metal Acceptor	false
O35	ZN	ZN- 400	2.35	0	Metal Acceptor	false
O31	O	HOH- 470	2.94	162.86	H-Bond (Protein Donor)	false
N11	O	HOH- 550	3.09	158.61	H-Bond (Ligand Donor)	false