scPDB - 3k9u entry

Protein Data Bank Entry:

PDB ID : 3k9u

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2009-10-16

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Spermidine N(1)-acetyltransferase
ID:	PAIA_THEAC
AC:	Q9HL57
Organism:	Thermoplasma acidophilum
Reign:	Archaea
TaxID:	273075
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	12 %
B	88 %

Ligand binding site composition:

B-Factor:	21.182
Number of residues:	43
Including
Standard Amino Acids:	42
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:	ACO
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.219	1167.750

% Hydrophobic	% Polar
46.82	53.18
According to VolSite

Ligand :

HET Code:	ACO
Formula:	C23H34N7O17P3S
Molecular weight:	805.539 g/mol
DrugBank ID:	-
Buried Surface Area:	72.85 %
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
32.1793	-29.3604	-13.5391

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
C6P	CG2	THR- 27	3.73	0	Hydrophobic	false
CH3	CD2	LEU- 89	4.16	0	Hydrophobic	false
CEP	CG	LEU- 92	3.59	0	Hydrophobic	false
N4P	O	LEU- 92	2.79	154.9	H-Bond (Ligand Donor)	false
O	N	LEU- 92	3.35	131.65	H-Bond (Protein Donor)	false
C6P	CD1	TYR- 93	3.38	0	Hydrophobic	false
C2P	CZ	TYR- 93	3.77	0	Hydrophobic	false
CEP	CG	LEU- 94	4.03	0	Hydrophobic	false
CAP	CD1	LEU- 94	4.09	0	Hydrophobic	false
O9P	N	LEU- 94	2.92	145.47	H-Bond (Protein Donor)	false
N6A	OG1	THR- 99	3.04	157.99	H-Bond (Ligand Donor)	false
CAP	CG2	THR- 99	3.78	0	Hydrophobic	false
O4A	N	HIS- 100	2.67	162.78	H-Bond (Protein Donor)	false
O1A	N	LYS- 102	2.79	148.57	H-Bond (Protein Donor)	false
O5A	N	GLY- 104	2.73	148.33	H-Bond (Protein Donor)	false
CH3	CB	LEU- 125	4.24	0	Hydrophobic	false
S1P	CG2	VAL- 127	4.09	0	Hydrophobic	false
O5P	ND2	ASN- 131	2.84	166.15	H-Bond (Protein Donor)	false
C1B	CB	PHE- 137	4.21	0	Hydrophobic	false
CCP	CD2	PHE- 137	3.36	0	Hydrophobic	false
CDP	CG	PHE- 137	4.04	0	Hydrophobic	false
S1P	CE2	TYR- 138	3.76	0	Hydrophobic	false
CH3	CZ	TYR- 138	4.1	0	Hydrophobic	false
O2B	NZ	LYS- 140	2.93	164.68	H-Bond (Protein Donor)	false
O9A	NZ	LYS- 140	2.72	160.04	H-Bond (Protein Donor)	false
C3B	CD	LYS- 140	4.48	0	Hydrophobic	false
O8A	NZ	LYS- 140	3.87	0	Ionic (Protein Cationic)	false
O9A	NZ	LYS- 140	2.72	0	Ionic (Protein Cationic)	false