scPDB - 2r7n entry

Protein Data Bank Entry:

PDB ID : 2r7n

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 2007-09-09

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase
ID:	PURP_METJA
AC:	Q57600
Organism:	Methanocaldococcus jannaschii
Reign:	Archaea
TaxID:	243232
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	46.288
Number of residues:	26
Including
Standard Amino Acids:	25
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.028	600.750

% Hydrophobic	% Polar
37.08	62.92
According to VolSite

Ligand :

HET Code:	ADP
Formula:	C10H12N5O10P2
Molecular weight:	424.177 g/mol
DrugBank ID:	-
Buried Surface Area:	63.49 %
Polar Surface area:	260.7 Å2

Number of
H-Bond Acceptors:	14
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
11.9891	10.1961	36.0106

Binding mode :

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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
C1'	CD1	ILE- 154	4.08	0	Hydrophobic	false
O1A	NZ	LYS- 156	2.77	159.79	H-Bond (Protein Donor)	false
N7	NZ	LYS- 156	2.81	138.87	H-Bond (Protein Donor)	false
O1A	NZ	LYS- 156	2.77	0	Ionic (Protein Cationic)	false
C5'	CE2	TYR- 166	3.81	0	Hydrophobic	false
N6	OE2	GLU- 199	2.73	151.55	H-Bond (Ligand Donor)	false
N6	O	GLU- 200	3.02	136.11	H-Bond (Ligand Donor)	false
N1	N	VAL- 202	2.92	141.16	H-Bond (Protein Donor)	false
O2'	OE1	GLU- 230	3.04	165.38	H-Bond (Ligand Donor)	false
C1'	CD1	TYR- 253	3.99	0	Hydrophobic	false
C4'	CB	TYR- 253	3.99	0	Hydrophobic	false
O3B	NE2	GLN- 297	3.32	150.12	H-Bond (Protein Donor)	false
C3'	CE1	PHE- 309	3.55	0	Hydrophobic	false
C2'	CZ	PHE- 309	3.82	0	Hydrophobic	false