scPDB - 1vhn entry

Protein Data Bank Entry:

PDB ID : 1vhn

Resolution :1.590 Å

Experimental Method : X-ray

Deposition Date : 2003-12-01

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	tRNA-dihydrouridine synthase
ID:	Q9WXV1_THEMA
AC:	Q9WXV1
Organism:	Thermotoga maritima
Reign:	Bacteria
TaxID:	243274
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	14.353
Number of residues:	43
Including
Standard Amino Acids:	40
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.270	378.000

% Hydrophobic	% Polar
48.21	51.79
According to VolSite

Ligand :

HET Code:	FMN
Formula:	C17H19N4O9P
Molecular weight:	454.328 g/mol
DrugBank ID:	DB03247
Buried Surface Area:	68.65 %
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
-1.63571	18.3005	10.9134

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- 10	4.2	0	Hydrophobic	false
O2'	O	PRO- 11	2.84	159.84	H-Bond (Ligand Donor)	false
C8M	SD	MET- 12	4.22	0	Hydrophobic	false
C2'	CG	MET- 12	4.33	0	Hydrophobic	false
C6	CB	MET- 12	3.69	0	Hydrophobic	false
C9	CG	MET- 12	3.77	0	Hydrophobic	false
O4	N	ALA- 13	3.38	128.24	H-Bond (Protein Donor)	false
N5	N	ALA- 13	2.91	158.16	H-Bond (Protein Donor)	false
C6	CB	ALA- 13	4.41	0	Hydrophobic	false
C7M	CE1	TYR- 15	3.56	0	Hydrophobic	false
O4	N	MET- 36	3.32	150.38	H-Bond (Protein Donor)	false
O2	NE2	GLN- 64	2.9	157.74	H-Bond (Protein Donor)	false
N3	OE1	GLN- 64	2.77	169.28	H-Bond (Ligand Donor)	false
N1	NZ	LYS- 132	3.08	152.94	H-Bond (Protein Donor)	false
O2	NZ	LYS- 132	3.11	143.44	H-Bond (Protein Donor)	false
O3'	NZ	LYS- 132	2.89	163.06	H-Bond (Protein Donor)	false
C4'	CE2	PHE- 168	3.76	0	Hydrophobic	false
O1P	N	ASP- 191	2.72	157.6	H-Bond (Protein Donor)	false
O3P	N	ILE- 192	3.19	170.19	H-Bond (Protein Donor)	false
C3'	CB	ALA- 213	3.6	0	Hydrophobic	false
C8M	CG	ARG- 214	3.6	0	Hydrophobic	false
O1P	NE	ARG- 214	3.42	132.82	H-Bond (Protein Donor)	false
O1P	NH2	ARG- 214	2.77	167.22	H-Bond (Protein Donor)	false
O2P	N	ARG- 214	2.97	161.67	H-Bond (Protein Donor)	false
O2P	NE	ARG- 214	2.85	162.88	H-Bond (Protein Donor)	false
O1P	CZ	ARG- 214	3.53	0	Ionic (Protein Cationic)	false
O2P	CZ	ARG- 214	3.83	0	Ionic (Protein Cationic)	false
O3P	O	HOH- 329	2.66	179.96	H-Bond (Protein Donor)	false
O3P	O	HOH- 330	2.69	179.96	H-Bond (Protein Donor)	false