scPDB - 2gyo entry

Protein Data Bank Entry:

PDB ID : 2gyo

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2006-05-09

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
ID:	FABH_ECOLI
AC:	P0A6R0
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	32.057
Number of residues:	34
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.614	394.875

% Hydrophobic	% Polar
60.68	39.32
According to VolSite

Ligand :

HET Code:	COA
Formula:	C21H32N7O16P3S
Molecular weight:	763.502 g/mol
DrugBank ID:	DB01992
Buried Surface Area:	52.81 %
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
44.5298	86.5907	64.3895

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
N1A	OG1	THR- 28	2.83	158.45	H-Bond (Protein Donor)	false
N6A	OG1	THR- 28	3.4	133.05	H-Bond (Ligand Donor)	false
C1B	CZ2	TRP- 32	4.15	0	Hydrophobic	false
CDP	CH2	TRP- 32	3.35	0	Hydrophobic	false
DuAr	DuAr	TRP- 32	3.49	0	Aromatic Face/Face	false
CDP	CG2	THR- 37	4.2	0	Hydrophobic	false
C2P	SG	CYS- 112	3.75	0	Hydrophobic	false
DuAr	CZ	ARG- 151	3.68	163.77	Pi/Cation	false
CAP	CD1	ILE- 156	4.34	0	Hydrophobic	false
S1P	CD2	LEU- 189	4.21	0	Hydrophobic	false
CEP	CE	MET- 207	4.29	0	Hydrophobic	false
O1A	ND2	ASN- 210	2.8	134.74	H-Bond (Protein Donor)	false
C6P	CG1	VAL- 212	4.26	0	Hydrophobic	false
S1P	CG1	VAL- 212	4.18	0	Hydrophobic	false
C6P	CB	ALA- 246	4.31	0	Hydrophobic	false
C2P	CB	ALA- 246	4.21	0	Hydrophobic	false
O5A	CZ	ARG- 249	3.2	0	Ionic (Protein Cationic)	false
O5A	NH1	ARG- 249	2.67	149.34	H-Bond (Protein Donor)	false
O5A	NH2	ARG- 249	2.89	136.97	H-Bond (Protein Donor)	false
O6A	NH1	ARG- 249	3.31	131.7	H-Bond (Protein Donor)	false
C6P	CD1	ILE- 250	3.91	0	Hydrophobic	false
S1P	CD1	PHE- 304	3.9	0	Hydrophobic	false