scPDB - 2o7p entry

Protein Data Bank Entry:

PDB ID : 2o7p

Resolution :3.000 Å

Experimental Method : X-ray

Deposition Date : 2006-12-11

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Riboflavin biosynthesis protein RibD
ID:	Q3ZUB0_ECOLX
AC:	Q3ZUB0
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	562
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	85.493
Number of residues:	40
Including
Standard Amino Acids:	40
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.240	556.875

% Hydrophobic	% Polar
56.36	43.64
According to VolSite

Ligand :

HET Code:	NAP
Formula:	C21H25N7O17P3
Molecular weight:	740.381 g/mol
DrugBank ID:	DB03461
Buried Surface Area:	60.94 %
Polar Surface area:	405.54 Å2

Number of
H-Bond Acceptors:	21
H-Bond Donors:	5
Rings:	5
Aromatic rings:	3
Anionic atoms:	4
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
78.0678	-64.9606	41.5585

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
C3N	CB	ALA- 162	4.39	0	Hydrophobic	false
C4D	SD	MET- 163	3.62	0	Hydrophobic	false
O3D	N	ALA- 164	3.1	152.98	H-Bond (Protein Donor)	false
O2D	N	ALA- 164	3.17	132.48	H-Bond (Protein Donor)	false
C2D	CH2	TRP- 170	3.98	0	Hydrophobic	false
DuAr	DuAr	TRP- 170	3.88	0	Aromatic Face/Face	false
O2A	OG	SER- 193	2.73	140.75	H-Bond (Protein Donor)	false
O5B	OG	SER- 193	3.21	128.54	H-Bond (Protein Donor)	false
C4B	CB	SER- 193	3.89	0	Hydrophobic	false
O2X	OG	SER- 194	2.79	153.51	H-Bond (Protein Donor)	false
C5B	CB	ALA- 195	4.25	0	Hydrophobic	false
C5D	CB	ALA- 195	4.19	0	Hydrophobic	false
C5N	CG2	THR- 196	3.87	0	Hydrophobic	false
C3D	CB	ALA- 199	4.26	0	Hydrophobic	false
C1B	CG2	ILE- 232	4.45	0	Hydrophobic	false
O3X	N	SER- 234	3.19	167.06	H-Bond (Protein Donor)	false
O2A	N	GLY- 301	3	144.28	H-Bond (Protein Donor)	false
C5B	CB	THR- 303	3.82	0	Hydrophobic	false
O1N	N	THR- 303	3.18	153.36	H-Bond (Protein Donor)	false
O1A	N	LEU- 304	2.81	169.75	H-Bond (Protein Donor)	false
C5B	CB	LEU- 304	4.39	0	Hydrophobic	false
C1B	CG	LEU- 304	4.36	0	Hydrophobic	false