scPDB - 3e4v entry

Protein Data Bank Entry:

PDB ID : 3e4v

Resolution :1.400 Å

Experimental Method : X-ray

Deposition Date : 2008-08-12

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Uncharacterized protein
ID:	Q1H3S7_METFK
AC:	Q1H3S7
Organism:	Methylobacillus flagellatus
Reign:	Bacteria
TaxID:	265072
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	84 %
B	16 %

Ligand binding site composition:

B-Factor:	13.142
Number of residues:	41
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.780	553.500

% Hydrophobic	% Polar
50.00	50.00
According to VolSite

Ligand :

HET Code:	FMN
Formula:	C17H19N4O9P
Molecular weight:	454.328 g/mol
DrugBank ID:	DB03247
Buried Surface Area:	83.85 %
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
30.7666	63.6102	11.0965

Binding mode :

What is Poseview ?

2D View
3D View

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
C7M	CD1	ILE- 19	3.91	0	Hydrophobic	false
O1P	ND2	ASN- 32	2.81	176.29	H-Bond (Protein Donor)	false
C2'	CE	MET- 34	4.34	0	Hydrophobic	false
C5'	CB	MET- 34	3.8	0	Hydrophobic	false
O2'	O	THR- 35	2.77	167.49	H-Bond (Ligand Donor)	false
O2'	N	THR- 35	3.18	146.62	H-Bond (Protein Donor)	false
C7	CG2	THR- 35	3.71	0	Hydrophobic	false
C8	CG2	THR- 35	3.89	0	Hydrophobic	false
C9	CB	THR- 35	4.15	0	Hydrophobic	false
O4	N	GLY- 37	3.2	129.87	H-Bond (Protein Donor)	false
N5	N	GLY- 37	3.04	152.87	H-Bond (Protein Donor)	false
O4	N	PHE- 38	2.85	155.48	H-Bond (Protein Donor)	false
N3	O	ILE- 52	2.83	146.08	H-Bond (Ligand Donor)	false
O2	N	GLY- 54	3.41	162.16	H-Bond (Protein Donor)	false
N1	NE1	TRP- 56	3.47	171.31	H-Bond (Protein Donor)	false
O3'	OD1	ASP- 57	2.86	158.53	H-Bond (Ligand Donor)	false
C5'	CB	ASP- 57	4.1	0	Hydrophobic	false
O3P	N	TYR- 58	2.77	155.46	H-Bond (Protein Donor)	false
O2P	OG	SER- 59	2.6	151.96	H-Bond (Protein Donor)	false
O2P	N	SER- 59	2.82	155.88	H-Bond (Protein Donor)	false
O4'	O	CYS- 88	2.74	152	H-Bond (Ligand Donor)	false
O3P	OG	SER- 89	2.75	168.76	H-Bond (Protein Donor)	false
O1P	N	GLY- 90	2.78	163.48	H-Bond (Protein Donor)	false
O5'	NZ	LYS- 95	3	132.56	H-Bond (Protein Donor)	false
O1P	NZ	LYS- 95	2.93	0	Ionic (Protein Cationic)	false
C7M	CB	HIS- 158	4.49	0	Hydrophobic	false
C7M	CZ	PHE- 164	4.04	0	Hydrophobic	false
C8	CE	MET- 177	4.49	0	Hydrophobic	false
C8M	SD	MET- 177	3.79	0	Hydrophobic	false
O4'	NZ	LYS- 179	2.8	164.05	H-Bond (Protein Donor)	false
C1'	CZ2	TRP- 180	3.55	0	Hydrophobic	false
O3P	O	HOH- 359	2.7	179.94	H-Bond (Protein Donor)	false