scPDB - 1rx0 entry

Protein Data Bank Entry:

PDB ID : 1rx0

Resolution :1.770 Å

Experimental Method : X-ray

Deposition Date : 2003-12-18

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Isobutyryl-CoA dehydrogenase, mitochondrial
ID:	ACAD8_HUMAN
AC:	Q9UKU7
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	1.3.99

Chains:

Chain Name:	Percentage of Residues within binding site
A	3 %
C	97 %

Ligand binding site composition:

B-Factor:	18.214
Number of residues:	44
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	1
Water Molecules:	6
Cofactors:	FAD
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.634	448.875

% Hydrophobic	% Polar
63.16	36.84
According to VolSite

Ligand :

HET Code:	2MC
Formula:	C25H36N7O17P3S
Molecular weight:	831.576 g/mol
DrugBank ID:	DB01675
Buried Surface Area:	55.16 %
Polar Surface area:	429.68 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	5
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	21

Mass center Coordinates

X	Y	Z
48.6218	-30.7597	44.2711

Binding mode :

What is Poseview ?

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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
C2M	CG1	ILE- 103	3.61	0	Hydrophobic	false
C2M	CE	MET- 106	4	0	Hydrophobic	false
C2P	CE2	TYR- 136	4.16	0	Hydrophobic	false
S1P	CD2	TYR- 136	3.52	0	Hydrophobic	false
C2M	CD2	TYR- 136	4.24	0	Hydrophobic	false
C2P	CD2	LEU- 138	4.05	0	Hydrophobic	false
N8P	O	SER- 145	2.86	157.55	H-Bond (Ligand Donor)	false
C6P	CB	ALA- 147	3.82	0	Hydrophobic	false
C5B	CG	PRO- 190	3.82	0	Hydrophobic	false
C4B	CD1	PHE- 244	4.44	0	Hydrophobic	false
C5B	CE1	PHE- 244	3.95	0	Hydrophobic	false
CAP	CZ	PHE- 244	3.99	0	Hydrophobic	false
C1B	CG2	VAL- 248	4.49	0	Hydrophobic	false
S1P	CD2	LEU- 251	4.33	0	Hydrophobic	false
N1A	ND2	ASN- 252	2.88	155.56	H-Bond (Protein Donor)	false
N6A	OD1	ASN- 252	2.76	160.52	H-Bond (Ligand Donor)	false
O9P	NH2	ARG- 255	3.08	153.43	H-Bond (Protein Donor)	false
O5P	NH2	ARG- 255	2.84	152.94	H-Bond (Protein Donor)	false
CDP	CZ	PHE- 283	3.8	0	Hydrophobic	false
O2	N	GLU- 376	2.84	154.49	H-Bond (Protein Donor)	false
C2M	CG	GLU- 376	4.43	0	Hydrophobic	false
CEP	CG1	VAL- 381	3.78	0	Hydrophobic	false
CEP	CD2	LEU- 385	3.52	0	Hydrophobic	false
O2A	NH1	ARG- 388	2.94	136.22	H-Bond (Protein Donor)	false
O2A	NH2	ARG- 388	2.81	141.76	H-Bond (Protein Donor)	false
O2A	CZ	ARG- 388	3.28	0	Ionic (Protein Cationic)	false
O2	O2'	FAD- 399	2.96	166.78	H-Bond (Protein Donor)	false
N4P	O	HOH- 9269	3.02	149.58	H-Bond (Ligand Donor)	false