scPDB - 1v25 entry

Protein Data Bank Entry:

PDB ID : 1v25

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2003-10-07

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Long-chain-fatty-acid--CoA ligase
ID:	LCFCS_THET8
AC:	Q5SKN9
Organism:	Thermus thermophilus
Reign:	Bacteria
TaxID:	300852
EC Number:	6.2.1.3

Chains:

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

Ligand binding site composition:

B-Factor:	16.374
Number of residues:	45
Including
Standard Amino Acids:	41
Non Standard Amino Acids:	1
Water Molecules:	3
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
1.014	1127.250

% Hydrophobic	% Polar
37.13	62.87
According to VolSite

Ligand :

HET Code:	ANP
Formula:	C10H13N6O12P3
Molecular weight:	502.164 g/mol
DrugBank ID:	-
Buried Surface Area:	72.16 %
Polar Surface area:	322.68 Å2

Number of
H-Bond Acceptors:	16
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
2.275	55.9676	158.408

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
O1G	N	VAL- 231	3.2	128.42	H-Bond (Protein Donor)	false
O2B	NE1	TRP- 234	3.05	153.4	H-Bond (Protein Donor)	false
N7	N	GLY- 302	3.36	122.63	H-Bond (Protein Donor)	false
N6	O	GLY- 323	2.86	145.74	H-Bond (Ligand Donor)	false
C2'	CE1	TYR- 324	3.93	0	Hydrophobic	false
C5'	CG	LEU- 326	3.95	0	Hydrophobic	false
C3'	CG	LEU- 326	3.86	0	Hydrophobic	false
O2A	N	THR- 327	3.05	169.32	H-Bond (Protein Donor)	false
O2A	OG1	THR- 327	2.98	167.95	H-Bond (Protein Donor)	false
O3'	OD2	ASP- 418	2.81	152.06	H-Bond (Ligand Donor)	false
O3'	OD1	ASP- 418	3.05	144.46	H-Bond (Ligand Donor)	false
O2'	OD1	ASP- 418	2.64	155.12	H-Bond (Ligand Donor)	false
O3'	NZ	LYS- 435	2.78	123.8	H-Bond (Protein Donor)	false
O1B	NZ	LYS- 439	2.67	156.05	H-Bond (Protein Donor)	false
O5'	NZ	LYS- 439	2.99	140.35	H-Bond (Protein Donor)	false
O1B	NZ	LYS- 439	2.67	0	Ionic (Protein Cationic)	false
O1A	NZ	LYS- 439	3.86	0	Ionic (Protein Cationic)	false
O1A	NE1	TRP- 444	2.75	173.57	H-Bond (Protein Donor)	false
C4'	CZ2	TRP- 444	3.57	0	Hydrophobic	false
O2A	MG	MG- 1001	2.55	0	Metal Acceptor	false