scPDB - 1b9i entry

Protein Data Bank Entry:

PDB ID : 1b9i

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 1999-02-11

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	3-amino-5-hydroxybenzoate synthase
ID:	RIFK_AMYMS
AC:	O52552
Organism:	Amycolatopsis mediterranei
Reign:	Bacteria
TaxID:	713604
EC Number:	4.2.1.144

Chains:

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

Ligand binding site composition:

B-Factor:	26.279
Number of residues:	35
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.266	273.375

% Hydrophobic	% Polar
46.91	53.09
According to VolSite

Ligand :

HET Code:	PXG
Formula:	C15H14N2O7P
Molecular weight:	365.255 g/mol
DrugBank ID:	-
Buried Surface Area:	62.24 %
Polar Surface area:	167.51 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	2
Rings:	2
Aromatic rings:	2
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
16.8428	36.5524	13.4853

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
OP2	N	GLY- 62	2.71	150.82	H-Bond (Protein Donor)	false
C5A	CB	THR- 63	4.44	0	Hydrophobic	false
OP1	OG1	THR- 63	2.52	172.91	H-Bond (Protein Donor)	false
OP1	N	THR- 63	2.76	137.41	H-Bond (Protein Donor)	false
C2A	CB	PHE- 88	4.14	0	Hydrophobic	false
C5A	CD2	PHE- 88	4.31	0	Hydrophobic	false
C4A	CD2	PHE- 88	3.63	0	Hydrophobic	false
C3	CB	PHE- 88	3.49	0	Hydrophobic	false
C5A	CB	SER- 90	3.71	0	Hydrophobic	false
C2A	CG1	VAL- 133	3.81	0	Hydrophobic	false
N1	OD2	ASP- 159	2.63	166.07	H-Bond (Ligand Donor)	false
C2A	CB	ALA- 161	4.12	0	Hydrophobic	false
C3	CB	ALA- 161	3.74	0	Hydrophobic	false
O3	NE2	HIS- 162	2.8	149.54	H-Bond (Protein Donor)	false
C5A	CB	SER- 183	4.36	0	Hydrophobic	false
OP2	OG	SER- 183	2.58	176.22	H-Bond (Protein Donor)	false
C11	CG	GLN- 185	4.01	0	Hydrophobic	false
OP2	O	HOH- 438	2.82	179.99	H-Bond (Protein Donor)	false