scPDB - 2j9f entry

Protein Data Bank Entry:

PDB ID : 2j9f

Resolution :1.880 Å

Experimental Method : X-ray

Deposition Date : 2006-11-07

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial	2-oxoisovalerate dehydrogenase subunit beta, mitochondrial
ID:	ODBA_HUMAN	ODBB_HUMAN
AC:	P12694	P21953
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	1.2.4.4

Chains:

Chain Name:	Percentage of Residues within binding site
A	75 %
B	2 %
D	23 %

Ligand binding site composition:

B-Factor:	12.349
Number of residues:	48
Including
Standard Amino Acids:	43
Non Standard Amino Acids:	1
Water Molecules:	4
Cofactors:
Metals:	MN

Cavity properties

Ligandability	Volume (Å3)
1.201	1113.750

% Hydrophobic	% Polar
51.52	48.48
According to VolSite

Ligand :

HET Code:	THV
Formula:	C16H24N4O8P2S
Molecular weight:	494.396 g/mol
DrugBank ID:	-
Buried Surface Area:	76.42 %
Polar Surface area:	245.55 Å2

Number of
H-Bond Acceptors:	11
H-Bond Donors:	2
Rings:	2
Aromatic rings:	2
Anionic atoms:	3
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	10

Mass center Coordinates

X	Y	Z
33.7427	66.0825	18.9221

Binding mode :

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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
C4A	CD1	LEU- 74	3.69	0	Hydrophobic	false
C5B	CD1	LEU- 74	3.71	0	Hydrophobic	false
N1'	OE2	GLU- 76	2.64	168.59	H-Bond (Ligand Donor)	false
C11	CZ	PHE- 85	3.69	0	Hydrophobic	false
C9	CE	MET- 87	3.98	0	Hydrophobic	false
C2A	CD1	TYR- 102	3.92	0	Hydrophobic	false
DuAr	DuAr	TYR- 102	3.52	0	Aromatic Face/Face	false
O1A	NE2	GLN- 112	2.78	160.58	H-Bond (Protein Donor)	false
O2B	OH	TYR- 113	2.53	165.42	H-Bond (Protein Donor)	false
C5B	CZ	TYR- 113	4.48	0	Hydrophobic	false
C9	CE2	TYR- 113	4.18	0	Hydrophobic	false
C10	CD2	TYR- 113	3.69	0	Hydrophobic	false
O2B	CZ	ARG- 114	3.68	0	Ionic (Protein Cationic)	false
O1B	CZ	ARG- 114	3.86	0	Ionic (Protein Cationic)	false
O2B	NH2	ARG- 114	2.86	177.71	H-Bond (Protein Donor)	false
O1B	NE	ARG- 114	2.92	163.55	H-Bond (Protein Donor)	false
O9	NE2	HIS- 146	2.79	171.02	H-Bond (Protein Donor)	false
C10	CB	SER- 162	3.96	0	Hydrophobic	false
N4'	O	SER- 162	2.84	168.03	H-Bond (Ligand Donor)	false
C4A	CD1	LEU- 164	3.89	0	Hydrophobic	false
S1	CD1	LEU- 164	4.38	0	Hydrophobic	false
C5'	CD1	LEU- 164	3.84	0	Hydrophobic	false
C2A	CB	LEU- 164	4.27	0	Hydrophobic	false
C5B	CD1	LEU- 164	3.74	0	Hydrophobic	false
N3'	N	LEU- 164	3.18	166.56	H-Bond (Protein Donor)	false
O2A	N	GLY- 194	2.97	147.56	H-Bond (Protein Donor)	false
O1A	N	ALA- 195	2.9	151.26	H-Bond (Protein Donor)	false
O1B	NH1	ARG- 220	2.84	149.94	H-Bond (Protein Donor)	false
O1B	NH2	ARG- 220	3.02	139.96	H-Bond (Protein Donor)	false
O1B	CZ	ARG- 220	3.35	0	Ionic (Protein Cationic)	false
O3B	ND2	ASN- 222	3.05	146.97	H-Bond (Protein Donor)	false
O1B	ND2	ASN- 222	3.44	129.86	H-Bond (Protein Donor)	false
C5A	CB	ALA- 225	4.15	0	Hydrophobic	false
C5A	CG1	ILE- 226	3.62	0	Hydrophobic	false
C4A	CD1	ILE- 226	3.89	0	Hydrophobic	false
O3B	MN	MN- 1401	2.24	0	Metal Acceptor	false
O2A	MN	MN- 1401	2.28	0	Metal Acceptor	false
O3B	O	HOH- 2203	3.04	179.98	H-Bond (Protein Donor)	false