scPDB - 1b87 entry

Protein Data Bank Entry:

PDB ID : 1b87

Resolution :2.700 Å

Experimental Method : X-ray

Deposition Date : 1999-02-09

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Aac(6')-Ii protein
ID:	Q47764_ENTFC
AC:	Q47764
Organism:	Enterococcus faecium
Reign:	Bacteria
TaxID:	1352
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	9.311
Number of residues:	37
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.565	850.500

% Hydrophobic	% Polar
42.86	57.14
According to VolSite

Ligand :

HET Code:	ACO
Formula:	C23H34N7O17P3S
Molecular weight:	805.539 g/mol
DrugBank ID:	-
Buried Surface Area:	55.28 %
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
53.4787	29.8616	24.8725

Binding mode :

What is Poseview ?

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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- 24	4.08	0	Hydrophobic	false
C6P	CZ2	TRP- 25	3.58	0	Hydrophobic	false
CEP	CG	LEU- 76	3.77	0	Hydrophobic	false
N4P	O	LEU- 76	3.38	153.07	H-Bond (Ligand Donor)	false
CEP	CG2	VAL- 78	4.2	0	Hydrophobic	false
CAP	CG2	VAL- 78	4.28	0	Hydrophobic	false
O9P	N	VAL- 78	2.81	139.44	H-Bond (Protein Donor)	false
CAP	CD	ARG- 83	4.08	0	Hydrophobic	false
C2B	CD	LYS- 84	4.17	0	Hydrophobic	false
O4A	N	LYS- 84	2.74	173.34	H-Bond (Protein Donor)	false
O1A	N	GLN- 86	2.73	144.58	H-Bond (Protein Donor)	false
O5A	N	GLY- 88	2.78	155.65	H-Bond (Protein Donor)	false
O2A	OG1	THR- 89	2.71	166.81	H-Bond (Protein Donor)	false
O2A	N	THR- 89	3.01	139.55	H-Bond (Protein Donor)	false
N6A	O	GLU- 141	2.88	153.06	H-Bond (Ligand Donor)	false
CDP	CB	PRO- 143	4.11	0	Hydrophobic	false
CCP	CE1	PHE- 146	3.81	0	Hydrophobic	false
CDP	CD2	PHE- 146	4.41	0	Hydrophobic	false
CEP	CE2	PHE- 146	4.19	0	Hydrophobic	false
C5B	CD1	PHE- 146	3.89	0	Hydrophobic	false
C2P	CZ	TYR- 147	4.09	0	Hydrophobic	false
S1P	CE2	TYR- 147	4.38	0	Hydrophobic	false
C1B	CD	LYS- 149	4.48	0	Hydrophobic	false
C4B	CD	LYS- 149	4.26	0	Hydrophobic	false
O3B	NZ	LYS- 149	3.39	120.78	H-Bond (Protein Donor)	false
O8A	NZ	LYS- 149	2.65	148	H-Bond (Protein Donor)	false
O8A	NZ	LYS- 149	2.65	0	Ionic (Protein Cationic)	false
N3A	O	HOH- 313	2.8	179.96	H-Bond (Protein Donor)	false
O5A	O	HOH- 323	2.82	137.76	H-Bond (Protein Donor)	false