scPDB - 1vyr entry

Protein Data Bank Entry:

PDB ID : 1vyr

Resolution :0.900 Å

Experimental Method : X-ray

Deposition Date : 2004-05-05

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Pentaerythritol tetranitrate reductase
ID:	P71278_ENTCL
AC:	P71278
Organism:	Enterobacter cloacae
Reign:	Bacteria
TaxID:	550
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	8.269
Number of residues:	38
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	1
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.460	789.750

% Hydrophobic	% Polar
39.74	60.26
According to VolSite

Ligand :

HET Code:	FMN
Formula:	C17H19N4O9P
Molecular weight:	454.328 g/mol
DrugBank ID:	DB03247
Buried Surface Area:	77.11 %
Polar Surface area:	217.05 Å2

Number of
H-Bond Acceptors:	12
H-Bond Donors:	4
Rings:	3
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
24.6704	9.40332	24.7776

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
C2'	CB	ALA- 23	4.29	0	Hydrophobic	false
O2'	O	PRO- 24	2.76	166.12	H-Bond (Ligand Donor)	false
C2'	CD2	LEU- 25	4.19	0	Hydrophobic	false
C8	CD2	LEU- 25	3.78	0	Hydrophobic	false
O4	OG1	THR- 26	2.68	161.89	H-Bond (Protein Donor)	false
N5	N	THR- 26	2.82	171.24	H-Bond (Protein Donor)	false
C6	CB	THR- 26	4.11	0	Hydrophobic	false
O4	N	ALA- 58	3.22	156.66	H-Bond (Protein Donor)	false
O2	NE2	GLN- 100	2.92	172.25	H-Bond (Protein Donor)	false
N3	OE1	GLN- 100	2.84	171.6	H-Bond (Ligand Donor)	false
O2	NH1	ARG- 233	2.83	150.99	H-Bond (Protein Donor)	false
O2'	NH1	ARG- 233	2.91	147.19	H-Bond (Protein Donor)	false
O3'	NH1	ARG- 233	3.38	126.88	H-Bond (Protein Donor)	false
O3'	NH2	ARG- 233	2.95	138.09	H-Bond (Protein Donor)	false
C4'	CD2	LEU- 275	3.76	0	Hydrophobic	false
C8M	CD1	LEU- 275	3.96	0	Hydrophobic	false
O1P	N	ALA- 302	2.85	136.05	H-Bond (Protein Donor)	false
O2P	N	GLY- 323	2.85	172.49	H-Bond (Protein Donor)	false
C8M	CG	ARG- 324	3.68	0	Hydrophobic	false
O1P	NH2	ARG- 324	2.83	170.78	H-Bond (Protein Donor)	false
O3P	NE	ARG- 324	2.86	158.34	H-Bond (Protein Donor)	false
O3P	N	ARG- 324	2.82	169.02	H-Bond (Protein Donor)	false
O1P	CZ	ARG- 324	3.72	0	Ionic (Protein Cationic)	false
O3P	CZ	ARG- 324	3.69	0	Ionic (Protein Cationic)	false
C7M	CD1	ILE- 327	4.2	0	Hydrophobic	false
C7M	CB	PHE- 350	3.95	0	Hydrophobic	false
C8M	CD2	PHE- 350	4.4	0	Hydrophobic	false
C7M	CZ	TYR- 351	3.54	0	Hydrophobic	false
O2P	O	HOH- 2781	2.78	179.99	H-Bond (Protein Donor)	false