scPDB - 4ku3 entry

Protein Data Bank Entry:

PDB ID : 4ku3

Resolution :1.970 Å

Experimental Method : X-ray

Deposition Date : 2013-05-21

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	3-oxoacyl-[ACP] synthase III
ID:	Q8PDX2_XANCP
AC:	Q8PDX2
Organism:	Xanthomonas campestris pv. campestris
Reign:	Bacteria
TaxID:	190485
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	4 %
B	96 %

Ligand binding site composition:

B-Factor:	37.965
Number of residues:	63
Including
Standard Amino Acids:	57
Non Standard Amino Acids:	0
Water Molecules:	6
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.755	540.000

% Hydrophobic	% Polar
59.38	40.63
According to VolSite

Ligand :

HET Code:	MYA
Formula:	C35H58N7O17P3S
Molecular weight:	973.858 g/mol
DrugBank ID:	DB02180
Buried Surface Area:	59.57 %
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:	32

Mass center Coordinates

X	Y	Z
-9.77954	14.554	-41.6201

Binding mode :

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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
C13	CG2	VAL- 62	4.08	0	Hydrophobic	false
C14	CG2	VAL- 62	3.94	0	Hydrophobic	false
C1X	CG2	VAL- 62	4.31	0	Hydrophobic	false
C12	CG1	VAL- 66	4.18	0	Hydrophobic	false
C14	CG1	VAL- 66	3.54	0	Hydrophobic	false
C4X	CG2	VAL- 66	3.98	0	Hydrophobic	false
C5X	CG1	VAL- 66	4.26	0	Hydrophobic	false
C14	CB	ALA- 67	3.87	0	Hydrophobic	false
C7M	CB	VAL- 111	3.97	0	Hydrophobic	false
CEM	CG1	VAL- 111	3.99	0	Hydrophobic	false
C5M	CG	GLU- 117	4.46	0	Hydrophobic	false
CFM	CG	GLU- 117	4.16	0	Hydrophobic	false
C8M	CG	GLU- 171	3.9	0	Hydrophobic	false
C9M	CB	GLU- 171	4.03	0	Hydrophobic	false
CAM	CB	ALA- 173	3.95	0	Hydrophobic	false
CDM	CG1	VAL- 176	4.3	0	Hydrophobic	false
O2X	NH1	ARG- 195	3	157.26	H-Bond (Protein Donor)	false
N6A	O	ARG- 195	3.22	161.37	H-Bond (Ligand Donor)	false
DuAr	CZ	ARG- 195	3.89	163.81	Pi/Cation	false
C13	CD1	LEU- 198	4.28	0	Hydrophobic	false
C6	CB	ALA- 199	3.47	0	Hydrophobic	false
C6	CG2	THR- 202	3.74	0	Hydrophobic	false
S1	CD2	LEU- 203	4.28	0	Hydrophobic	false
C4M	CD2	LEU- 203	3.98	0	Hydrophobic	false
C6M	CD2	LEU- 203	4.22	0	Hydrophobic	false
C9M	CB	LEU- 203	4.41	0	Hydrophobic	false
CAM	CD1	LEU- 203	4	0	Hydrophobic	false
CDM	CD1	LEU- 203	4.44	0	Hydrophobic	false
C3M	SG	CYS- 239	3.94	0	Hydrophobic	false
C2	SG	CYS- 239	3.9	0	Hydrophobic	false
CCM	CD1	LEU- 243	4.17	0	Hydrophobic	false
S1	CE	MET- 246	3.89	0	Hydrophobic	false
CFM	CB	MET- 246	4.36	0	Hydrophobic	false
C4M	SD	MET- 246	3.77	0	Hydrophobic	false
C2	CG2	THR- 248	4.02	0	Hydrophobic	false
C13	CB	THR- 250	4.36	0	Hydrophobic	false
N6A	OG1	THR- 250	3.03	155.98	H-Bond (Ligand Donor)	false
O1A	CZ	ARG- 251	3.29	0	Ionic (Protein Cationic)	false
C2	CD1	LEU- 253	3.65	0	Hydrophobic	false
N4	O	HOH- 511	2.83	153.38	H-Bond (Ligand Donor)	false
O5	O	HOH- 524	2.91	151.92	H-Bond (Protein Donor)	false