scPDB - 2pja entry

Protein Data Bank Entry:

PDB ID : 2pja

Resolution :1.700 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
B	100 %

Ligand binding site composition:

B-Factor:	16.550
Number of residues:	45
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	1
Water Molecules:	5
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
0.028	310.500

% Hydrophobic	% Polar
33.70	66.30
According to VolSite

Ligand :

HET Code:	33Z
Formula:	C31H37N5O7P
Molecular weight:	622.629 g/mol
DrugBank ID:	-
Buried Surface Area:	56.85 %
Polar Surface area:	221.14 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	5
Rings:	3
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	16

Mass center Coordinates

X	Y	Z
21.8986	24.9635	98.8915

Binding mode :

What is Poseview ?

2D View
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
O33	NH2	ARG- 71	2.95	154.66	H-Bond (Protein Donor)	false
O26	NH2	ARG- 127	3.3	131.16	H-Bond (Protein Donor)	false
O26	NH1	ARG- 127	2.73	162.1	H-Bond (Protein Donor)	false
O26	CZ	ARG- 127	3.45	0	Ionic (Protein Cationic)	false
O13	ND2	ASN- 144	2.91	164.55	H-Bond (Protein Donor)	false
O14	CZ	ARG- 145	3.51	0	Ionic (Protein Cationic)	false
O13	CZ	ARG- 145	3.8	0	Ionic (Protein Cationic)	false
O14	NH1	ARG- 145	3.36	131.55	H-Bond (Protein Donor)	false
O14	NH2	ARG- 145	2.8	161.18	H-Bond (Protein Donor)	false
O13	NH1	ARG- 145	2.87	169.01	H-Bond (Protein Donor)	false
C39	CB	GLU- 163	3.89	0	Hydrophobic	false
C38	CG2	THR- 164	3.83	0	Hydrophobic	false
C29	CE1	TYR- 198	3.76	0	Hydrophobic	false
C5	CD2	LEU- 203	3.34	0	Hydrophobic	false
C30	CD1	ILE- 247	4.23	0	Hydrophobic	false
C50	CD1	ILE- 247	3.41	0	Hydrophobic	false
C5	CG2	ILE- 247	3.66	0	Hydrophobic	false
N31	OH	TYR- 248	3.23	139.93	H-Bond (Ligand Donor)	false
C23	CZ	TYR- 248	4.28	0	Hydrophobic	false
O14	OH	TYR- 248	2.69	162.74	H-Bond (Protein Donor)	false
N12	O	ALA- 250	3.35	155.69	H-Bond (Ligand Donor)	false
N9	OD1	ASP- 255	3.42	132.87	H-Bond (Ligand Donor)	false
N9	OD2	ASP- 255	3.1	159.97	H-Bond (Ligand Donor)	false
N11	OD1	ASP- 255	2.8	168.59	H-Bond (Ligand Donor)	false
C10	OD1	ASP- 255	3.55	0	Ionic (Ligand Cationic)	false
C10	OD2	ASP- 255	3.93	0	Ionic (Ligand Cationic)	false
C6	CB	THR- 268	4.11	0	Hydrophobic	false
C7	CG2	THR- 268	4.35	0	Hydrophobic	false
C5	CG2	THR- 268	4.17	0	Hydrophobic	false
O25	OE2	GLU- 270	2.66	163.59	H-Bond (Protein Donor)	false
C29	CZ	PHE- 279	3.89	0	Hydrophobic	false
O25	ZN	ZN- 500	2.24	0	Metal Acceptor	false
N11	O	HOH- 538	2.88	160.31	H-Bond (Ligand Donor)	false
O33	O	HOH- 685	2.73	152.21	H-Bond (Protein Donor)	false
N12	O	HOH- 709	2.88	129	H-Bond (Ligand Donor)	false