scPDB - 2bdz entry

Protein Data Bank Entry:

PDB ID : 2bdz

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2005-10-21

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Mexicain
ID:	MEX1_JACME
AC:	P84346
Organism:	Jacaratia mexicana
Reign:	Eukaryota
TaxID:	309130
EC Number:	3.4.22

Chains:

Chain Name:	Percentage of Residues within binding site
A	4 %
B	96 %

Ligand binding site composition:

B-Factor:	10.224
Number of residues:	27
Including
Standard Amino Acids:	26
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.247	1184.625

% Hydrophobic	% Polar
35.33	64.67
According to VolSite

Ligand :

HET Code:	E64
Formula:	C15H29N5O5
Molecular weight:	359.421 g/mol
DrugBank ID:	DB04276
Buried Surface Area:	48.88 %
Polar Surface area:	182.2 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	6
Rings:	0
Aromatic rings:	0
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
2.387	34.4906	21.9648

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
O2	NE2	GLN- 19	2.68	142.44	H-Bond (Protein Donor)	false
N5	O	ASP- 64	2.7	158.81	H-Bond (Ligand Donor)	false
O4	N	GLY- 66	2.88	149.78	H-Bond (Protein Donor)	false
N2	O	GLY- 66	2.88	177.52	H-Bond (Ligand Donor)	false
C13	CE1	TYR- 67	3.85	0	Hydrophobic	false
C10	CG1	VAL- 133	3.83	0	Hydrophobic	false
C10	CB	THR- 157	4.03	0	Hydrophobic	false
N1	O	ASP- 158	2.92	166.33	H-Bond (Ligand Donor)	false