scPDB - 4ku2 entry

Protein Data Bank Entry:

PDB ID : 4ku2

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	2 %
B	98 %

Ligand binding site composition:

B-Factor:	44.148
Number of residues:	62
Including
Standard Amino Acids:	55
Non Standard Amino Acids:	0
Water Molecules:	7
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.416	459.000

% Hydrophobic	% Polar
56.62	43.38
According to VolSite

Ligand :

HET Code:	MYA
Formula:	C35H58N7O17P3S
Molecular weight:	973.858 g/mol
DrugBank ID:	DB02180
Buried Surface Area:	60.5 %
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
-12.4671	14.8342	-42.8006

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
C13	CG1	VAL- 62	4.19	0	Hydrophobic	false
C14	CG1	VAL- 62	4.02	0	Hydrophobic	false
C1X	CG2	VAL- 62	3.76	0	Hydrophobic	false
C12	CG1	VAL- 66	4.23	0	Hydrophobic	false
C14	CG1	VAL- 66	3.49	0	Hydrophobic	false
C14	CB	ALA- 67	3.93	0	Hydrophobic	false
O2X	NH2	ARG- 195	2.79	154.5	H-Bond (Protein Donor)	false
N6A	O	ARG- 195	3.12	159.62	H-Bond (Ligand Donor)	false
DuAr	CZ	ARG- 195	3.82	164.13	Pi/Cation	false
C13	CD2	LEU- 198	4.03	0	Hydrophobic	false
C6	CB	ALA- 199	4.23	0	Hydrophobic	false
C6	CG2	THR- 202	4.11	0	Hydrophobic	false
S1	SG	CYS- 239	3.73	0	Hydrophobic	false
C2	CE	MET- 246	4.38	0	Hydrophobic	false
C13	CB	THR- 250	4.25	0	Hydrophobic	false
N6A	OG1	THR- 250	2.97	157.21	H-Bond (Ligand Donor)	false
O1A	CZ	ARG- 251	3.44	0	Ionic (Protein Cationic)	false
S1	CD1	LEU- 253	3.61	0	Hydrophobic	false
C5M	CD2	LEU- 253	3.84	0	Hydrophobic	false
CAM	CD1	ILE- 258	3.31	0	Hydrophobic	false
CFM	CB	ALA- 261	3.94	0	Hydrophobic	false
CDM	CB	ILE- 284	4.35	0	Hydrophobic	false
O2M	NE2	HIS- 285	3.42	131.25	H-Bond (Protein Donor)	false
CCM	CB	HIS- 285	4.41	0	Hydrophobic	false
CEM	CB	HIS- 285	4.48	0	Hydrophobic	false
C6	CG1	VAL- 287	4.12	0	Hydrophobic	false
C9M	CG2	VAL- 287	4.15	0	Hydrophobic	false
CAM	CB	HIS- 291	3.83	0	Hydrophobic	false
CBM	CB	PHE- 295	4.27	0	Hydrophobic	false
CDM	CG	PHE- 295	4.49	0	Hydrophobic	false
O2M	ND2	ASN- 315	3.2	132.05	H-Bond (Protein Donor)	false
CFM	CB	LEU- 343	3.61	0	Hydrophobic	false
C4M	CG2	ILE- 345	4.47	0	Hydrophobic	false
C6M	CD1	ILE- 345	3.86	0	Hydrophobic	false
C8M	CD1	ILE- 345	4.47	0	Hydrophobic	false
C9M	CG2	ILE- 345	4.27	0	Hydrophobic	false
CFM	CB	ILE- 345	4.22	0	Hydrophobic	false
CEM	CG2	ILE- 345	3.51	0	Hydrophobic	false
C4M	CD2	LEU- 349	3.87	0	Hydrophobic	false
CFM	SG	CYS- 351	4.25	0	Hydrophobic	false
CFM	CE	MET- 353	3.64	0	Hydrophobic	false
N4	O	HOH- 509	2.91	149.27	H-Bond (Ligand Donor)	false
O5	O	HOH- 576	3.05	154.59	H-Bond (Protein Donor)	false
O7A	O	HOH- 670	3.27	122.97	H-Bond (Protein Donor)	false