scPDB - 5dn1 entry

Protein Data Bank Entry:

PDB ID : 5dn1

Resolution :1.950 Å

Experimental Method : X-ray

Deposition Date : 2015-09-09

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:	HIS4_STRCO
AC:	P16250
Organism:	Streptomyces coelicolor / M145)
Reign:	Bacteria
TaxID:	100226
EC Number:	5.3.1.16

Chains:

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

Ligand binding site composition:

B-Factor:	26.633
Number of residues:	37
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.160	452.250

% Hydrophobic	% Polar
39.55	60.45
According to VolSite

Ligand :

HET Code:	AMZ
Formula:	C9H13N4O8P
Molecular weight:	336.195 g/mol
DrugBank ID:	DB01700
Buried Surface Area:	68.73 %
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
7.23818	48.4327	9.98582

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
C1	CG1	VAL- 52	4.02	0	Hydrophobic	false
O2	OG	SER- 81	2.69	160.24	H-Bond (Protein Donor)	false
C	CB	SER- 81	4.13	0	Hydrophobic	false
O4	N	GLY- 83	2.73	130.23	H-Bond (Protein Donor)	false
OP1	NH2	ARG- 85	3.48	145.66	H-Bond (Protein Donor)	false
O4	NE	ARG- 85	2.81	144.79	H-Bond (Protein Donor)	false
O4	NH2	ARG- 85	2.93	136.59	H-Bond (Protein Donor)	false
O4	CZ	ARG- 85	3.28	0	Ionic (Protein Cationic)	false
OP2	N	GLY- 104	2.8	138.57	H-Bond (Protein Donor)	false
OP1	N	THR- 105	3	153.91	H-Bond (Protein Donor)	false
OP2	N	THR- 105	3.26	137.19	H-Bond (Protein Donor)	false
N2	O	GLY- 140	3.31	150.68	H-Bond (Ligand Donor)	false
C2	CZ2	TRP- 141	4.16	0	Hydrophobic	false
OP2	O	HOH- 453	2.93	179.96	H-Bond (Protein Donor)	false