scPDB - 2r0n entry

Protein Data Bank Entry:

PDB ID : 2r0n

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2007-08-20

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Glutaryl-CoA dehydrogenase, mitochondrial
ID:	GCDH_HUMAN
AC:	Q92947
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	1.3.8.6

Chains:

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

Ligand binding site composition:

B-Factor:	32.614
Number of residues:	51
Including
Standard Amino Acids:	48
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:	FAD
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.357	604.125

% Hydrophobic	% Polar
51.96	48.04
According to VolSite

Ligand :

HET Code:	TGC
Formula:	C25H35N7O19P3S2
Molecular weight:	894.632 g/mol
DrugBank ID:	-
Buried Surface Area:	53.63 %
Polar Surface area:	495.11 Å2

Number of
H-Bond Acceptors:	25
H-Bond Donors:	5
Rings:	3
Aromatic rings:	2
Anionic atoms:	5
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	24

Mass center Coordinates

X	Y	Z
73.2848	11.2834	41.2422

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
O2'	NH1	ARG- 94	3.11	122.24	H-Bond (Protein Donor)	false
C3'	CG2	VAL- 99	3.61	0	Hydrophobic	false
C2'	CD1	LEU- 103	3.81	0	Hydrophobic	false
S81	CE1	PHE- 133	3.99	0	Hydrophobic	false
C73	CD2	LEU- 135	3.84	0	Hydrophobic	false
N68	O	SER- 142	3.27	142.78	H-Bond (Ligand Donor)	false
C57	CG	PRO- 144	4.05	0	Hydrophobic	false
C61	CG	PRO- 144	3.74	0	Hydrophobic	false
C3'	CB	THR- 170	4.45	0	Hydrophobic	false
C19	CD2	LEU- 239	4.25	0	Hydrophobic	false
C18	CB	LEU- 239	3.92	0	Hydrophobic	false
C15	CD1	PHE- 243	3.83	0	Hydrophobic	false
C53	CE1	PHE- 243	3.34	0	Hydrophobic	false
C18	CE1	PHE- 243	4	0	Hydrophobic	false
C57	CZ	PHE- 243	3.31	0	Hydrophobic	false
S81	CD2	LEU- 246	3.57	0	Hydrophobic	false
O51	NH2	ARG- 250	3.1	156.14	H-Bond (Protein Donor)	false
S3'	CD1	TYR- 369	3.42	0	Hydrophobic	false
C3'	CE1	TYR- 369	3.99	0	Hydrophobic	false
O1'	N	GLU- 370	3.09	129.92	H-Bond (Protein Donor)	false
S3'	CG	GLU- 370	4.04	0	Hydrophobic	false
C44	CG2	ILE- 375	4.15	0	Hydrophobic	false
C46	CE2	PHE- 390	4.33	0	Hydrophobic	false
C44	CE2	PHE- 390	4.27	0	Hydrophobic	false
N71	O4'	FAD- 400	3.31	172.3	H-Bond (Ligand Donor)	false
O1'	O2'	FAD- 400	2.55	145.59	H-Bond (Protein Donor)	false
S3'	C9A	FAD- 400	4.44	0	Hydrophobic	false
O38	O	HOH- 503	2.88	179.95	H-Bond (Protein Donor)	false