scPDB - 4c2j entry

Protein Data Bank Entry:

PDB ID : 4c2j

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2013-08-19

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, mitochondrial
ID:	THIM_HUMAN
AC:	P42765
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	2.3.1.16

Chains:

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

Ligand binding site composition:

B-Factor:	16.962
Number of residues:	43
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	1
Water Molecules:	5
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.614	661.500

% Hydrophobic	% Polar
62.76	37.24
According to VolSite

Ligand :

HET Code:	COA
Formula:	C21H32N7O16P3S
Molecular weight:	763.502 g/mol
DrugBank ID:	DB01992
Buried Surface Area:	43.28 %
Polar Surface area:	426.11 Å2

Number of
H-Bond Acceptors:	21
H-Bond Donors:	6
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	18

Mass center Coordinates

X	Y	Z
-4.39723	-42.1346	41.5365

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
S1P	SG	CSO- 92	3.98	0	Hydrophobic	false
CEP	CH2	TRP- 149	3.76	0	Hydrophobic	false
C6P	CD1	LEU- 152	4.24	0	Hydrophobic	false
S1P	CG	MET- 161	3.91	0	Hydrophobic	false
O2B	NH1	ARG- 224	2.9	139.89	H-Bond (Protein Donor)	false
O2B	NH2	ARG- 224	3.31	127.34	H-Bond (Protein Donor)	false
DuAr	CZ	ARG- 224	3.35	166.25	Pi/Cation	false
N6A	OG1	THR- 227	2.97	145.7	H-Bond (Ligand Donor)	false
C1B	CD2	LEU- 235	3.89	0	Hydrophobic	false
CEP	CG1	VAL- 238	4.42	0	Hydrophobic	false
CDP	CE1	PHE- 239	4.23	0	Hydrophobic	false
CEP	CZ	PHE- 239	4.19	0	Hydrophobic	false
C4B	CB	ALA- 247	4.01	0	Hydrophobic	false
CCP	CB	ALA- 247	3.96	0	Hydrophobic	false
CDP	CB	ALA- 250	4.12	0	Hydrophobic	false
N8P	O	SER- 251	2.93	134.03	H-Bond (Ligand Donor)	false
CAP	CG2	VAL- 253	4.12	0	Hydrophobic	false
C6P	CG2	VAL- 253	4.23	0	Hydrophobic	false
S1P	CE	MET- 292	3.66	0	Hydrophobic	false
C2P	CB	ALA- 322	3.91	0	Hydrophobic	false
S1P	CE2	PHE- 323	3.84	0	Hydrophobic	false
N6A	O	HOH- 2170	2.95	133.71	H-Bond (Ligand Donor)	false
N4P	O	HOH- 2218	2.93	165.83	H-Bond (Ligand Donor)	false