scPDB - 2d5n entry

Protein Data Bank Entry:

PDB ID : 2d5n

Resolution :2.970 Å

Experimental Method : X-ray

Deposition Date : 2005-11-02

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:	RIBD_BACSU
AC:	P17618
Organism:	Bacillus subtilis
Reign:	Bacteria
TaxID:	224308
EC Number:	1.1.1.193

Chains:

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

Ligand binding site composition:

B-Factor:	62.187
Number of residues:	45
Including
Standard Amino Acids:	45
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.247	344.250

% Hydrophobic	% Polar
35.29	64.71
According to VolSite

Ligand :

HET Code:	NDP
Formula:	C21H26N7O17P3
Molecular weight:	741.389 g/mol
DrugBank ID:	DB02338
Buried Surface Area:	55.44 %
Polar Surface area:	404.9 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	5
Rings:	5
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
38.9046	63.6787	69.0033

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
O7N	N	ALA- 153	2.87	167.69	H-Bond (Protein Donor)	false
N7N	O	ALA- 153	2.7	136.33	H-Bond (Ligand Donor)	false
C3N	CB	ILE- 160	4.27	0	Hydrophobic	false
C5D	CD1	ILE- 160	3.85	0	Hydrophobic	false
C4B	CG2	VAL- 193	4.11	0	Hydrophobic	false
C1B	CG2	VAL- 193	4.37	0	Hydrophobic	false
O5B	N	GLY- 194	3.09	122.06	H-Bond (Protein Donor)	false
O1A	OG1	THR- 195	2.86	166.73	H-Bond (Protein Donor)	false
C5N	CG2	THR- 195	4.33	0	Hydrophobic	false
O2D	OD1	ASP- 199	3.4	164.1	H-Bond (Ligand Donor)	false
O3X	N	THR- 221	3.19	127.58	H-Bond (Protein Donor)	false
N1A	O	ILE- 270	2.7	161.86	H-Bond (Ligand Donor)	false
O1N	N	SER- 293	3.22	126.68	H-Bond (Protein Donor)	false
C5D	CB	SER- 293	4.32	0	Hydrophobic	false
C5B	CB	ALA- 294	3.68	0	Hydrophobic	false
O1N	N	ALA- 294	3.39	157.98	H-Bond (Protein Donor)	false
O2A	N	VAL- 295	2.97	156.63	H-Bond (Protein Donor)	false
N6A	OG	SER- 298	2.62	127.96	H-Bond (Ligand Donor)	false
C4D	CB	PRO- 323	4.23	0	Hydrophobic	false