scPDB - 2dvl entry

Protein Data Bank Entry:

PDB ID : 2dvl

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2006-07-31

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Acyl-CoA dehydrogenase
ID:	Q5SH14_THET8
AC:	Q5SH14
Organism:	Thermus thermophilus
Reign:	Bacteria
TaxID:	300852
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	95 %
B	5 %

Ligand binding site composition:

B-Factor:	35.278
Number of residues:	38
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.306	1417.500

% Hydrophobic	% Polar
54.52	45.48
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	42.6 %
Polar Surface area:	381.7 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	7
Rings:	6
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
-30.5621	-5.34643	-3.97468

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
N3	O	PHE- 121	2.86	168.04	H-Bond (Ligand Donor)	false
O2	N	LEU- 123	3.07	143.05	H-Bond (Protein Donor)	false
N1	OG1	THR- 124	2.65	159.79	H-Bond (Protein Donor)	false
O2	N	THR- 124	2.77	173.27	H-Bond (Protein Donor)	false
C1'	CG2	THR- 124	3.85	0	Hydrophobic	false
C3'	CG2	THR- 124	4.35	0	Hydrophobic	false
O1A	OG	SER- 130	2.76	158.42	H-Bond (Protein Donor)	false
O1A	N	SER- 130	3.03	150.52	H-Bond (Protein Donor)	false
C5'	CB	SER- 130	4.32	0	Hydrophobic	false
C8M	CE3	TRP- 154	3.93	0	Hydrophobic	false
C1'	CB	TRP- 154	3.53	0	Hydrophobic	false
C9A	CB	TRP- 154	3.58	0	Hydrophobic	false
O4	OG1	THR- 156	3.3	148.16	H-Bond (Protein Donor)	false
O4	N	THR- 156	3.12	170.99	H-Bond (Protein Donor)	false
N5	OG1	THR- 156	3	135.27	H-Bond (Protein Donor)	false
C7M	CD	LYS- 194	4.25	0	Hydrophobic	false
C7M	CD1	LEU- 197	4.07	0	Hydrophobic	false
C6	CG2	THR- 202	3.82	0	Hydrophobic	false
N1A	NE2	GLN- 272	2.89	177.98	H-Bond (Protein Donor)	false
C7M	CG2	VAL- 351	3.94	0	Hydrophobic	false
C8M	CG2	VAL- 351	3.66	0	Hydrophobic	false
C9	CB	TYR- 355	3.99	0	Hydrophobic	false
O2B	OG1	THR- 358	2.59	168.29	H-Bond (Protein Donor)	false
C2B	CG2	THR- 358	3.85	0	Hydrophobic	false
O2B	OE1	GLU- 360	3.05	134.37	H-Bond (Ligand Donor)	false