scPDB - 1wdk entry

Protein Data Bank Entry:

PDB ID : 1wdk

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2004-05-17

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	3-ketoacyl-CoA thiolase
ID:	FADA_PSEFR
AC:	P28790
Organism:	Pseudomonas fragi
Reign:	Bacteria
TaxID:	296
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	23.990
Number of residues:	40
Including
Standard Amino Acids:	40
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.053	347.625

% Hydrophobic	% Polar
66.02	33.98
According to VolSite

Ligand :

HET Code:	ACO
Formula:	C23H34N7O17P3S
Molecular weight:	805.539 g/mol
DrugBank ID:	-
Buried Surface Area:	42.65 %
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:	20

Mass center Coordinates

X	Y	Z
0.484431	21.0305	88.9897

Binding mode :

What is Poseview ?

2D View
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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
O1A	NZ	LYS- 22	3.88	0	Ionic (Protein Cationic)	false
S1P	SG	CYS- 95	4.41	0	Hydrophobic	false
CH3	SG	CYS- 95	3.26	0	Hydrophobic	false
C2P	CB	MET- 151	3.66	0	Hydrophobic	false
O2B	NH1	ARG- 215	3.34	124.68	H-Bond (Protein Donor)	false
DuAr	CZ	ARG- 215	3.74	156.68	Pi/Cation	false
C1B	CD2	LEU- 226	4.21	0	Hydrophobic	false
CEP	CB	ALA- 229	4	0	Hydrophobic	false
CDP	CE2	PHE- 230	4.15	0	Hydrophobic	false
CEP	CZ	PHE- 230	3.67	0	Hydrophobic	false
C5B	CB	ALA- 239	4.26	0	Hydrophobic	false
CCP	CB	ALA- 239	4.21	0	Hydrophobic	false
CEP	CB	ALA- 239	4.19	0	Hydrophobic	false
C6P	CB	SER- 242	4.07	0	Hydrophobic	false
N4P	OG	SER- 243	3.38	158.62	H-Bond (Ligand Donor)	false
CAP	CG1	ILE- 245	4.48	0	Hydrophobic	false
CH3	CE	MET- 284	3.25	0	Hydrophobic	false
CH3	CB	ALA- 314	4.09	0	Hydrophobic	false
S1P	CB	ALA- 314	3.34	0	Hydrophobic	false
C6P	CE1	PHE- 315	3.91	0	Hydrophobic	false
C2P	CE2	PHE- 315	3.48	0	Hydrophobic	false
CH3	SG	CYS- 377	3.58	0	Hydrophobic	false