scPDB - 2iyg entry

Protein Data Bank Entry:

PDB ID : 2iyg

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2006-07-17

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	AppA, antirepressor of ppsR, sensor of blue light
ID:	Q3J677_RHOS4
AC:	Q3J677
Organism:	Rhodobacter sphaeroides
Reign:	Bacteria
TaxID:	272943
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	21.711
Number of residues:	26
Including
Standard Amino Acids:	26
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.705	317.250

% Hydrophobic	% Polar
56.38	43.62
According to VolSite

Ligand :

HET Code:	FMN
Formula:	C17H19N4O9P
Molecular weight:	454.328 g/mol
DrugBank ID:	DB03247
Buried Surface Area:	57.93 %
Polar Surface area:	217.05 Å2

Number of
H-Bond Acceptors:	12
H-Bond Donors:	4
Rings:	3
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
29.1198	47.4662	7.20952

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
C8M	CD1	ILE- 37	3.62	0	Hydrophobic	false
C9	CG2	ILE- 37	3.75	0	Hydrophobic	false
C4'	CG2	THR- 40	3.9	0	Hydrophobic	false
N3	OD1	ASN- 45	3.01	175.49	H-Bond (Ligand Donor)	false
O4	ND2	ASN- 45	3.17	156.26	H-Bond (Protein Donor)	false
C6	CD2	LEU- 54	4.36	0	Hydrophobic	false
C7M	CD2	LEU- 54	4	0	Hydrophobic	false
C7M	CG	PHE- 61	3.57	0	Hydrophobic	false
O4	NE2	GLN- 63	2.94	134.83	H-Bond (Protein Donor)	false
N5	NE2	GLN- 63	3.01	143.99	H-Bond (Protein Donor)	false
C3'	CB	HIS- 78	4.34	0	Hydrophobic	false
C6	CG2	ILE- 79	4.36	0	Hydrophobic	false
C9A	CG1	ILE- 79	3.68	0	Hydrophobic	false
C2'	CG1	ILE- 79	3.91	0	Hydrophobic	false
C8M	CB	ASP- 82	4.18	0	Hydrophobic	false
C9	CB	ASP- 82	4.43	0	Hydrophobic	false
O2'	OD2	ASP- 82	2.75	164.32	H-Bond (Ligand Donor)	false
C8M	CB	ARG- 84	4.23	0	Hydrophobic	false