scPDB - 4tx9 entry

Protein Data Bank Entry:

PDB ID : 4tx9

Resolution :1.600 Å

Experimental Method : X-ray

Deposition Date : 2014-07-02

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Phosphoribosyl isomerase A
ID:	B5I4P8_9ACTN
AC:	B5I4P8
Organism:	Streptomyces sviceus ATCC 29083
Reign:	Bacteria
TaxID:	463191
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	19.166
Number of residues:	38
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.634	432.000

% Hydrophobic	% Polar
48.44	51.56
According to VolSite

Ligand :

HET Code:	AMZ
Formula:	C9H13N4O8P
Molecular weight:	336.195 g/mol
DrugBank ID:	DB01700
Buried Surface Area:	70.47 %
Polar Surface area:	218.85 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	4
Rings:	2
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	5

Mass center Coordinates

X	Y	Z
32.442	23.7104	21.7844

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
N2	O	GLY- 27	3.03	168.24	H-Bond (Ligand Donor)	false
C1	CG1	VAL- 56	3.88	0	Hydrophobic	false
C	CG1	VAL- 56	4.29	0	Hydrophobic	false
O2	OG	SER- 85	2.74	170.1	H-Bond (Protein Donor)	false
C	CB	SER- 85	3.94	0	Hydrophobic	false
OP2	N	GLY- 87	2.71	153.59	H-Bond (Protein Donor)	false
OP2	NE	ARG- 89	2.96	138.96	H-Bond (Protein Donor)	false
OP2	NH2	ARG- 89	2.82	144.62	H-Bond (Protein Donor)	false
OP2	CZ	ARG- 89	3.3	0	Ionic (Protein Cationic)	false
O4	N	GLY- 108	2.96	147.17	H-Bond (Protein Donor)	false
OP1	N	THR- 109	2.88	160.09	H-Bond (Protein Donor)	false
OP1	OG1	THR- 109	2.62	159.89	H-Bond (Protein Donor)	false
O1	OD2	ASP- 134	2.75	145.59	H-Bond (Ligand Donor)	false
N2	O	GLY- 144	3.05	138.43	H-Bond (Ligand Donor)	false
O4	O	HOH- 518	2.66	150.72	H-Bond (Protein Donor)	false