scPDB - 1ps9 entry

Protein Data Bank Entry:

PDB ID : 1ps9

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2003-06-20

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	2,4-dienoyl-CoA reductase
ID:	FADH_ECOLI
AC:	P42593
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	1.3.1.34

Chains:

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

Ligand binding site composition:

B-Factor:	29.741
Number of residues:	52
Including
Standard Amino Acids:	49
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:	FMN
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.279	1069.875

% Hydrophobic	% Polar
48.58	51.42
According to VolSite

Ligand :

HET Code:	MDE
Formula:	C33H52N7O18P3S2
Molecular weight:	991.853 g/mol
DrugBank ID:	DB03698
Buried Surface Area:	45.42 %
Polar Surface area:	478.48 Å2

Number of
H-Bond Acceptors:	23
H-Bond Donors:	6
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	2
Rule of Five Violation:	3
Rotatable Bonds:	31

Mass center Coordinates

X	Y	Z
24.2228	5.41284	18.1471

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
CB1	CB	HIS- 26	4.36	0	Hydrophobic	false
SG	CB	HIS- 26	3.43	0	Hydrophobic	false
CB1	CD2	LEU- 102	3.88	0	Hydrophobic	false
CB1	CG2	THR- 104	4.32	0	Hydrophobic	false
C5B	CG2	ILE- 123	4.07	0	Hydrophobic	false
CDP	CD1	ILE- 123	3.92	0	Hydrophobic	false
C2'	CG	GLU- 164	4.42	0	Hydrophobic	false
CB	CZ	TYR- 166	4.44	0	Hydrophobic	false
N8P	O	HIS- 252	2.97	142.91	H-Bond (Ligand Donor)	false
N4P	ND1	HIS- 252	3.12	160.27	H-Bond (Ligand Donor)	false
N6A	O	GLU- 253	3.47	133.85	H-Bond (Ligand Donor)	false
OAP	NH2	ARG- 255	3.13	150.14	H-Bond (Protein Donor)	false
C2P	CG2	ILE- 259	3.64	0	Hydrophobic	false
S1P	CD1	ILE- 259	4.43	0	Hydrophobic	false
C3'	CD1	LEU- 342	4.39	0	Hydrophobic	false
C7'	CD1	LEU- 342	3.8	0	Hydrophobic	false
S1P	CD2	LEU- 342	3.94	0	Hydrophobic	false
CDP	CE1	PHE- 346	4.25	0	Hydrophobic	false
CEP	CE1	PHE- 346	3.92	0	Hydrophobic	false
CCP	CZ	PHE- 346	3.6	0	Hydrophobic	false
C9'	CD1	PHE- 346	3.36	0	Hydrophobic	false
O7B	NZ	LYS- 566	3.22	121.52	H-Bond (Protein Donor)	false
O7B	NZ	LYS- 566	3.22	0	Ionic (Protein Cationic)	false
O9B	NZ	LYS- 566	3.71	0	Ionic (Protein Cationic)	false
CEP	CG2	THR- 574	3.48	0	Hydrophobic	false
C9'	CG2	THR- 574	4.41	0	Hydrophobic	false
O9P	NE1	TRP- 577	2.96	147.9	H-Bond (Protein Donor)	false
S1P	C1'	FMN- 702	4.25	0	Hydrophobic	false
C2'	C1'	FMN- 702	3.98	0	Hydrophobic	false
C5'	C6	FMN- 702	4.38	0	Hydrophobic	false
C3'	C9A	FMN- 702	3.95	0	Hydrophobic	false