scPDB - 5kp2 entry

Protein Data Bank Entry:

PDB ID : 5kp2

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2016-07-01

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	3-oxoacyl-[acyl-carrier-protein] synthase 3 protein 2
ID:	FABH2_VIBCH
AC:	Q9KLJ3
Organism:	Vibrio cholerae serotype O1
Reign:	Bacteria
TaxID:	243277
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	27.543
Number of residues:	28
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.829	421.875

% Hydrophobic	% Polar
55.20	44.80
According to VolSite

Ligand :

HET Code:	COA
Formula:	C21H32N7O16P3S
Molecular weight:	763.502 g/mol
DrugBank ID:	DB01992
Buried Surface Area:	41.62 %
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
-9.59444	-5.62292	6.78977

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
N1A	OG1	THR- 31	3.12	156.93	H-Bond (Protein Donor)	false
N6A	OG1	THR- 31	3.2	138.8	H-Bond (Ligand Donor)	false
C1B	CZ2	TRP- 35	3.75	0	Hydrophobic	false
C5B	CZ2	TRP- 35	3.99	0	Hydrophobic	false
DuAr	DuAr	TRP- 35	3.46	0	Aromatic Face/Face	false
DuAr	CZ	ARG- 152	3.45	168.42	Pi/Cation	false
S1P	CZ	PHE- 158	4.32	0	Hydrophobic	false
S1P	CD2	LEU- 191	4.07	0	Hydrophobic	false
C6P	CZ	PHE- 214	3.74	0	Hydrophobic	false
S1P	CE2	PHE- 214	4.16	0	Hydrophobic	false
C2P	CG2	ILE- 219	4.42	0	Hydrophobic	false
CDP	CE2	PHE- 220	4.26	0	Hydrophobic	false
CAP	CD2	PHE- 220	3.6	0	Hydrophobic	false
C2P	CB	ALA- 253	3.85	0	Hydrophobic	false
CDP	CB	ARG- 256	3.29	0	Hydrophobic	false
C2P	CZ	PHE- 311	4.29	0	Hydrophobic	false