scPDB - 5a89 entry

Protein Data Bank Entry:

PDB ID : 5a89

Resolution :1.650 Å

Experimental Method : X-ray

Deposition Date : 2015-07-13

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 RibF
ID:	RIBF_CORAM
AC:	Q59263
Organism:	Corynebacterium ammoniagenes
Reign:	Bacteria
TaxID:	1697
EC Number:	2.7.1.26

Chains:

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

Ligand binding site composition:

B-Factor:	18.339
Number of residues:	47
Including
Standard Amino Acids:	43
Non Standard Amino Acids:	2
Water Molecules:	2
Cofactors:	ADP
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.757	293.625

% Hydrophobic	% Polar
64.37	35.63
According to VolSite

Ligand :

HET Code:	FMN
Formula:	C17H19N4O9P
Molecular weight:	454.328 g/mol
DrugBank ID:	DB03247
Buried Surface Area:	85.27 %
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
4.89587	-23.3919	-16.3034

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
O2P	N	ALA- 197	2.89	162.31	H-Bond (Protein Donor)	false
O3P	N	GLY- 198	3.32	120.44	H-Bond (Protein Donor)	false
O4'	NH1	ARG- 199	2.9	157.74	H-Bond (Protein Donor)	false
O5'	NH1	ARG- 199	3.43	121.31	H-Bond (Protein Donor)	false
O3P	N	ARG- 199	3.06	150.67	H-Bond (Protein Donor)	false
C5'	CG	ARG- 199	3.58	0	Hydrophobic	false
O3P	N	GLY- 200	3.2	146.83	H-Bond (Protein Donor)	false
C2'	CD1	LEU- 204	4.35	0	Hydrophobic	false
C4'	CD1	LEU- 204	3.92	0	Hydrophobic	false
C8M	CG2	THR- 208	3.71	0	Hydrophobic	false
O1P	ND2	ASN- 210	3.21	133.34	H-Bond (Protein Donor)	false
O2P	ND2	ASN- 210	3.2	149.97	H-Bond (Protein Donor)	false
C6	CG2	VAL- 224	3.66	0	Hydrophobic	false
C7M	CG1	VAL- 224	3.71	0	Hydrophobic	false
C7M	CB	ALA- 251	3.63	0	Hydrophobic	false
C1'	CB	SER- 253	4.22	0	Hydrophobic	false
C9	CB	SER- 253	3.44	0	Hydrophobic	false
O2	OG1	THR- 259	3.21	134.05	H-Bond (Protein Donor)	false
O2	N	THR- 259	2.87	158.57	H-Bond (Protein Donor)	false
C2'	CE2	PHE- 260	4.47	0	Hydrophobic	false
C4'	CE2	PHE- 260	4.47	0	Hydrophobic	false
O3'	OE1	GLU- 268	2.51	157.61	H-Bond (Ligand Donor)	false
C8M	CB	PHE- 270	4	0	Hydrophobic	false
O4	NH1	ARG- 292	2.86	166.97	H-Bond (Protein Donor)	false
O4	NH2	ARG- 292	3.4	135.22	H-Bond (Protein Donor)	false
N5	NH2	ARG- 292	2.97	131.8	H-Bond (Protein Donor)	false
N3	O	GLU- 295	2.68	174.43	H-Bond (Ligand Donor)	false
O4	N	GLU- 295	3.18	151.89	H-Bond (Protein Donor)	false
C6	CG	MET- 307	3.93	0	Hydrophobic	false
C9	CE	MET- 307	3.66	0	Hydrophobic	false
C7M	CB	ASP- 310	4.01	0	Hydrophobic	false
O1P	MG	MG- 341	1.92	0	Metal Acceptor	false
O2P	O	HOH- 2026	2.58	179.98	H-Bond (Protein Donor)	false