scPDB - 2zyn entry

Protein Data Bank Entry:

PDB ID : 2zyn

Resolution :1.700 Å

Experimental Method : X-ray

Deposition Date : 2009-01-27

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Periplasmic binding protein
ID:	Q9AJF5_THEVU
AC:	Q9AJF5
Organism:	Thermoactinomyces vulgaris
Reign:	Bacteria
TaxID:	2026
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	15.449
Number of residues:	47
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	0
Water Molecules:	8
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.883	951.750

% Hydrophobic	% Polar
45.04	54.96
According to VolSite

Ligand :

HET Code:	BCD
Formula:	C42H70O35
Molecular weight:	1134.984 g/mol
DrugBank ID:	DB03995
Buried Surface Area:	50.46 %
Polar Surface area:	554.05 Å2

Number of
H-Bond Acceptors:	35
H-Bond Donors:	21
Rings:	9
Aromatic rings:	0
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
-18.6284	4.64003	-27.0142

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
O32	OD1	ASN- 26	2.59	137.78	H-Bond (Ligand Donor)	false
O32	ND2	ASN- 26	2.84	128.69	H-Bond (Protein Donor)	false
O23	NE2	GLN- 32	3.46	139.9	H-Bond (Protein Donor)	false
C33	CD2	LEU- 58	3.98	0	Hydrophobic	false
C55	CD1	LEU- 59	4.5	0	Hydrophobic	false
C26	CD2	LEU- 59	4.42	0	Hydrophobic	false
C36	CB	LEU- 59	3.88	0	Hydrophobic	false
C35	CD2	LEU- 59	3.55	0	Hydrophobic	false
O36	O	LEU- 59	2.63	132.62	H-Bond (Ligand Donor)	false
C34	CG	PRO- 81	3.77	0	Hydrophobic	false
O25	OD2	ASP- 83	3.48	132.1	H-Bond (Ligand Donor)	false
O35	OD2	ASP- 83	2.7	173.64	H-Bond (Ligand Donor)	false
O35	OD1	ASP- 83	3.38	124.87	H-Bond (Ligand Donor)	false
O26	NH1	ARG- 84	2.76	150.92	H-Bond (Protein Donor)	false
C26	CD	ARG- 84	3.93	0	Hydrophobic	false
O24	OE1	GLU- 129	2.57	160.3	H-Bond (Ligand Donor)	false
O64	ND2	ASN- 173	3.26	129.95	H-Bond (Protein Donor)	false
O65	ND2	ASN- 173	3.22	126.99	H-Bond (Protein Donor)	false
C14	CE2	TYR- 175	4.21	0	Hydrophobic	false
C44	CG	TYR- 175	3.83	0	Hydrophobic	false
C15	CD1	TYR- 175	3.61	0	Hydrophobic	false
C24	CZ	TYR- 175	4.09	0	Hydrophobic	false
C64	CD2	TYR- 175	3.73	0	Hydrophobic	false
C63	CZ	TYR- 176	4.37	0	Hydrophobic	false
C64	CE1	TYR- 176	4.06	0	Hydrophobic	false
C61	CB	ALA- 230	4.22	0	Hydrophobic	false
C62	CB	ALA- 230	3.82	0	Hydrophobic	false
C23	CB	TRP- 250	3.85	0	Hydrophobic	false
C33	CD2	TRP- 250	4.33	0	Hydrophobic	false
C14	CZ2	TRP- 250	3.55	0	Hydrophobic	false
C24	CH2	TRP- 250	3.99	0	Hydrophobic	false
C63	CE2	TRP- 250	3.63	0	Hydrophobic	false
C25	SD	MET- 350	4.13	0	Hydrophobic	false
C35	CE2	TRP- 360	4.31	0	Hydrophobic	false
C65	CE3	TRP- 360	3.52	0	Hydrophobic	false
C16	CB	TRP- 360	3.82	0	Hydrophobic	false
C25	CZ2	TRP- 360	3.91	0	Hydrophobic	false
C45	CD2	TRP- 360	3.8	0	Hydrophobic	false
C66	CB	TRP- 360	4.17	0	Hydrophobic	false
O65	ND2	ASN- 364	3.29	149.17	H-Bond (Protein Donor)	false
O63	O	HOH- 406	2.68	179.98	H-Bond (Protein Donor)	false
O63	O	HOH- 490	2.91	179.94	H-Bond (Protein Donor)	false
O62	O	HOH- 700	2.84	179.96	H-Bond (Protein Donor)	false
O61	O	HOH- 715	3.03	179.97	H-Bond (Protein Donor)	false