scPDB - 3d2m entry

Protein Data Bank Entry:

PDB ID : 3d2m

Resolution :2.210 Å

Experimental Method : X-ray

Deposition Date : 2008-05-08

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Amino-acid acetyltransferase
ID:	Q5FAK7_NEIG1
AC:	Q5FAK7
Organism:	Neisseria gonorrhoeae
Reign:	Bacteria
TaxID:	242231
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	42.411
Number of residues:	33
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.601	445.500

% Hydrophobic	% Polar
47.73	52.27
According to VolSite

Ligand :

HET Code:	COA
Formula:	C21H32N7O16P3S
Molecular weight:	763.502 g/mol
DrugBank ID:	DB01992
Buried Surface Area:	52.03 %
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
38.8798	4.08315	17.4051

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	CD1	LEU- 307	4.03	0	Hydrophobic	false
C6P	CG2	ILE- 312	4.3	0	Hydrophobic	false
CDP	CG	LEU- 357	3.92	0	Hydrophobic	false
CDP	CG2	VAL- 359	4.33	0	Hydrophobic	false
O9P	N	VAL- 359	3.13	169.05	H-Bond (Protein Donor)	false
CAP	CG	GLN- 364	4.19	0	Hydrophobic	false
O4A	N	ASP- 365	2.99	167.36	H-Bond (Protein Donor)	false
O2A	N	GLY- 367	2.83	135.69	H-Bond (Protein Donor)	false
O3A	N	GLY- 369	3.17	123.12	H-Bond (Protein Donor)	false
O5A	N	GLY- 369	3.03	148.04	H-Bond (Protein Donor)	false
O1A	N	GLU- 370	3.13	153.94	H-Bond (Protein Donor)	false
S1P	CB	SER- 392	3.59	0	Hydrophobic	false
CEP	CG2	THR- 395	3.53	0	Hydrophobic	false
C2P	CB	THR- 395	3.47	0	Hydrophobic	false
O5P	OG1	THR- 395	2.54	168.31	H-Bond (Protein Donor)	false
O5B	NE1	TRP- 398	3.18	165.06	H-Bond (Protein Donor)	false
CCP	CE2	TRP- 398	3.93	0	Hydrophobic	false
CEP	CD2	TRP- 398	4.16	0	Hydrophobic	false
C2P	CE1	PHE- 399	3.81	0	Hydrophobic	false