scPDB - 2jdd entry

Protein Data Bank Entry:

PDB ID : 2jdd

Resolution :1.600 Å

Experimental Method : X-ray

Deposition Date : 2007-01-06

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Probable acetyltransferase
ID:	Q65LG7_BACLD
AC:	Q65LG7
Organism:	Bacillus licheniformis
Reign:	Bacteria
TaxID:	279010
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	12.820
Number of residues:	37
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.147	796.500

% Hydrophobic	% Polar
36.44	63.56
According to VolSite

Ligand :

HET Code:	ACO
Formula:	C23H34N7O17P3S
Molecular weight:	805.539 g/mol
DrugBank ID:	-
Buried Surface Area:	59.16 %
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:	20

Mass center Coordinates

X	Y	Z
14.0986	4.449	6.0051

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
C6P	CG2	ILE- 19	3.82	0	Hydrophobic	false
C6P	CD2	LEU- 20	3.71	0	Hydrophobic	false
C2P	CD2	LEU- 20	4.28	0	Hydrophobic	false
CDP	CG	MET- 75	3.97	0	Hydrophobic	false
N4P	O	MET- 75	2.86	137.47	H-Bond (Ligand Donor)	false
O	N	MET- 75	3.38	160.05	H-Bond (Protein Donor)	false
O5A	OG1	THR- 77	2.94	167.54	H-Bond (Protein Donor)	false
O9P	N	THR- 77	2.85	171.2	H-Bond (Protein Donor)	false
CDP	CB	THR- 77	4.4	0	Hydrophobic	false
CAP	CB	THR- 77	4.3	0	Hydrophobic	false
CAP	CD	ARG- 82	4.02	0	Hydrophobic	false
O2B	OE1	GLU- 83	2.72	154.8	H-Bond (Ligand Donor)	false
O4A	N	GLU- 83	2.88	167.32	H-Bond (Protein Donor)	false
O7A	NZ	LYS- 85	3.07	145.01	H-Bond (Protein Donor)	false
O1A	N	LYS- 85	2.94	143.24	H-Bond (Protein Donor)	false
O7A	NZ	LYS- 85	3.07	0	Ionic (Protein Cationic)	false
O9A	NZ	LYS- 85	3.91	0	Ionic (Protein Cationic)	false
C5B	CD	LYS- 85	4.33	0	Hydrophobic	false
O5A	N	GLY- 87	2.92	159.09	H-Bond (Protein Donor)	false
O2A	OG	SER- 88	2.62	154.82	H-Bond (Protein Donor)	false
O2A	N	SER- 88	2.91	148.14	H-Bond (Protein Donor)	false
S1P	SG	CYS- 108	4.07	0	Hydrophobic	false
CH3	SG	CYS- 108	3.57	0	Hydrophobic	false
C2P	CD	ARG- 111	3.93	0	Hydrophobic	false
S1P	CG	ARG- 111	4.24	0	Hydrophobic	false
N6A	O	SER- 113	2.9	157.05	H-Bond (Ligand Donor)	false
CEP	CB	ALA- 114	4.1	0	Hydrophobic	false
CCP	CE1	TYR- 117	3.72	0	Hydrophobic	false
CDP	CE2	TYR- 117	4.39	0	Hydrophobic	false
CEP	CD2	TYR- 117	3.91	0	Hydrophobic	false
C5B	CD1	TYR- 117	3.79	0	Hydrophobic	false
S1P	CE2	TYR- 118	3.87	0	Hydrophobic	false
O3B	NZ	LYS- 120	3.42	156.19	H-Bond (Protein Donor)	false
O8A	NZ	LYS- 120	2.82	137.98	H-Bond (Protein Donor)	false
O8A	NZ	LYS- 120	2.82	0	Ionic (Protein Cationic)	false
C4B	CB	LYS- 120	4.25	0	Hydrophobic	false
O5A	O	HOH- 2074	2.78	158.76	H-Bond (Protein Donor)	false