scPDB - 4r87 entry

Protein Data Bank Entry:

PDB ID : 4r87

Resolution :2.610 Å

Experimental Method : X-ray

Deposition Date : 2014-08-29

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:	ATDA_VIBCH
AC:	Q9KL03
Organism:	Vibrio cholerae serotype O1
Reign:	Bacteria
TaxID:	243277
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	35.337
Number of residues:	34
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.802	769.500

% Hydrophobic	% Polar
44.30	55.70
According to VolSite

Ligand :

HET Code:	COA
Formula:	C21H32N7O16P3S
Molecular weight:	763.502 g/mol
DrugBank ID:	DB01992
Buried Surface Area:	45.66 %
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
44.8649	160.068	29.907

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	CB	TYR- 30	4.15	0	Hydrophobic	false
N4P	O	ILE- 87	2.84	148	H-Bond (Ligand Donor)	false
C6P	CG1	ILE- 88	4.35	0	Hydrophobic	false
CDP	CD1	ILE- 89	4.09	0	Hydrophobic	false
O9P	N	ILE- 89	2.92	161.41	H-Bond (Protein Donor)	false
CAP	CG	GLN- 94	3.86	0	Hydrophobic	false
O9P	NE2	GLN- 94	3.31	124.61	H-Bond (Protein Donor)	false
O4A	N	GLY- 95	3.02	149.81	H-Bond (Protein Donor)	false
O1A	N	GLY- 97	2.82	137.52	H-Bond (Protein Donor)	false
O7A	NH2	ARG- 100	3.25	132.84	H-Bond (Protein Donor)	false
O7A	NH1	ARG- 100	2.69	167.05	H-Bond (Protein Donor)	false
O9A	NH2	ARG- 100	2.99	157.9	H-Bond (Protein Donor)	false
O7A	CZ	ARG- 100	3.41	0	Ionic (Protein Cationic)	false
O9A	CZ	ARG- 100	4	0	Ionic (Protein Cationic)	false
S1P	CG1	VAL- 123	3.81	0	Hydrophobic	false
O5P	ND2	ASN- 127	3.03	136.92	H-Bond (Protein Donor)	false
C1B	CG	LYS- 129	3.82	0	Hydrophobic	false
C4B	CG	LYS- 129	4.03	0	Hydrophobic	false
CEP	CB	ALA- 130	4.44	0	Hydrophobic	false
O3B	NE2	HIS- 132	3.21	130.5	H-Bond (Protein Donor)	false
O9A	NE2	HIS- 132	2.72	160.09	H-Bond (Protein Donor)	false
C5B	CD1	LEU- 133	3.96	0	Hydrophobic	false
CCP	CD1	LEU- 133	3.68	0	Hydrophobic	false
S1P	CE2	TYR- 134	4.08	0	Hydrophobic	false