scPDB - 1dub entry

Protein Data Bank Entry:

PDB ID : 1dub

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 1996-06-10

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Enoyl-CoA hydratase, mitochondrial
ID:	ECHM_RAT
AC:	P14604
Organism:	Rattus norvegicus
Reign:	Eukaryota
TaxID:	10116
EC Number:	4.2.1.17

Chains:

Chain Name:	Percentage of Residues within binding site
E	86 %
F	14 %

Ligand binding site composition:

B-Factor:	20.666
Number of residues:	42
Including
Standard Amino Acids:	42
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.374	438.750

% Hydrophobic	% Polar
73.85	26.15
According to VolSite

Ligand :

HET Code:	CAA
Formula:	C25H36N7O18P3S
Molecular weight:	847.576 g/mol
DrugBank ID:	DB03059
Buried Surface Area:	57.28 %
Polar Surface area:	446.75 Å2

Number of
H-Bond Acceptors:	23
H-Bond Donors:	5
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	22

Mass center Coordinates

X	Y	Z
93.2238	74.8374	178.628

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
C1B	CB	ALA- 57	4.24	0	Hydrophobic	false
C5B	CG	LEU- 58	3.84	0	Hydrophobic	false
CCP	CD1	LEU- 58	3.33	0	Hydrophobic	false
O4A	NZ	LYS- 92	3.22	155.19	H-Bond (Protein Donor)	false
O4A	NZ	LYS- 92	3.22	0	Ionic (Protein Cationic)	false
N6A	O	ALA- 96	3.43	141.39	H-Bond (Ligand Donor)	false
N4P	O	ALA- 96	2.91	161.03	H-Bond (Ligand Donor)	false
CEP	CB	ALA- 96	4.38	0	Hydrophobic	false
N6A	O	ALA- 98	2.87	141.77	H-Bond (Ligand Donor)	false
S1P	CB	ALA- 98	4.33	0	Hydrophobic	false
C2	CB	ALA- 98	3.73	0	Hydrophobic	false
O1	N	ALA- 98	3.35	173.41	H-Bond (Protein Donor)	false
N1A	N	ILE- 100	3.13	170.13	H-Bond (Protein Donor)	false
C2P	CD1	ILE- 100	4.41	0	Hydrophobic	false
S1P	CG1	ILE- 100	4.41	0	Hydrophobic	false
O7A	NZ	LYS- 101	3.26	164.75	H-Bond (Protein Donor)	false
O7A	NZ	LYS- 101	3.26	0	Ionic (Protein Cationic)	false
S1P	CE	MET- 103	3.57	0	Hydrophobic	false
C2	CE	MET- 103	3.95	0	Hydrophobic	false
C4	CD2	LEU- 117	3.72	0	Hydrophobic	false
CCP	CE2	TYR- 137	3.95	0	Hydrophobic	false
CDP	CZ	TYR- 137	4.25	0	Hydrophobic	false
CEP	CD2	TYR- 137	4	0	Hydrophobic	false
CEP	CD1	LEU- 139	3.41	0	Hydrophobic	false
O1	N	GLY- 141	2.8	139.75	H-Bond (Protein Donor)	false
C6P	CG	PRO- 163	4.12	0	Hydrophobic	false
C2	CG	GLU- 164	3.81	0	Hydrophobic	false
S1P	CG	GLU- 164	4.15	0	Hydrophobic	false
C2P	CG	LEU- 167	4.13	0	Hydrophobic	false
S1P	CD1	LEU- 167	3.6	0	Hydrophobic	false
C2	CE1	PHE- 263	4.33	0	Hydrophobic	false
C4	CE1	PHE- 263	3.62	0	Hydrophobic	false
C2B	CZ	PHE- 279	4.28	0	Hydrophobic	false
O2B	NZ	LYS- 282	3.41	159.07	H-Bond (Protein Donor)	false
O7A	NZ	LYS- 282	3.9	0	Ionic (Protein Cationic)	false
O8A	NZ	LYS- 282	3.94	0	Ionic (Protein Cationic)	false