scPDB - 4zwp entry

Protein Data Bank Entry:

PDB ID : 4zwp

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 2015-05-19

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Xaa-Pro dipeptidase
ID:	PEPQ_ALTSX
AC:	Q44238
Organism:	Alteromonas sp
Reign:	Bacteria
TaxID:	232
EC Number:	3.4.13.9

Chains:

Chain Name:	Percentage of Residues within binding site
A	8 %
B	92 %

Ligand binding site composition:

B-Factor:	33.013
Number of residues:	26
Including
Standard Amino Acids:	24
Non Standard Amino Acids:	2
Water Molecules:	0
Cofactors:
Metals:	MN MN

Cavity properties

Ligandability	Volume (Å3)
0.162	516.375

% Hydrophobic	% Polar
44.44	55.56
According to VolSite

Ligand :

HET Code:	M44
Formula:	C6H16N2O2P
Molecular weight:	179.177 g/mol
DrugBank ID:	-
Buried Surface Area:	67.66 %
Polar Surface area:	74 Å2

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

Mass center Coordinates

X	Y	Z
68.2519	-28.4442	150.84

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
C6	CD1	PHE- 212	3.76	0	Hydrophobic	false
C5	CE2	PHE- 212	3.32	0	Hydrophobic	false
C5	CD1	ILE- 215	3.81	0	Hydrophobic	false
C2	CB	HIS- 332	4.26	0	Hydrophobic	false
C6	CG1	VAL- 342	3.89	0	Hydrophobic	false
O1	NE2	HIS- 343	2.65	168.63	H-Bond (Protein Donor)	false
N1	OE1	GLU- 381	2.89	129.91	H-Bond (Ligand Donor)	false
C2	CD	ARG- 418	4.5	0	Hydrophobic	false
O1	MN	MN- 502	2.63	0	Metal Acceptor	false
O2	MN	MN- 502	2.31	0	Metal Acceptor	false