scPDB - 3gfy entry

Protein Data Bank Entry:

PDB ID : 3gfy

Resolution :2.600 Å

Experimental Method : X-ray

Deposition Date : 2009-02-27

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:	A6T8V8_KLEP7
AC:	A6T8V8
Organism:	Klebsiella pneumoniae subsp. pneumoniae
Reign:	Bacteria
TaxID:	272620
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	23.294
Number of residues:	27
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.741	533.250

% Hydrophobic	% Polar
53.16	46.84
According to VolSite

Ligand :

HET Code:	FMN
Formula:	C17H19N4O9P
Molecular weight:	454.328 g/mol
DrugBank ID:	DB03247
Buried Surface Area:	63.88 %
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
-37.8234	19.3079	-33.7051

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
C9A	CD2	LEU- 23	3.94	0	Hydrophobic	false
C6	CD2	LEU- 23	4.04	0	Hydrophobic	false
C8	CD1	LEU- 23	3.74	0	Hydrophobic	false
O3P	NE	ARG- 26	2.8	140.89	H-Bond (Protein Donor)	false
O3P	CZ	ARG- 26	3.79	0	Ionic (Protein Cationic)	false
O4'	NZ	LYS- 30	3.22	149.99	H-Bond (Protein Donor)	false
O2P	NZ	LYS- 30	3.79	0	Ionic (Protein Cationic)	false
N3	OD1	ASN- 31	2.79	167.83	H-Bond (Ligand Donor)	false
O4	ND2	ASN- 31	2.9	163.2	H-Bond (Protein Donor)	false
C7M	CD1	LEU- 40	3.96	0	Hydrophobic	false
C7M	CG	PHE- 47	3.74	0	Hydrophobic	false
N5	NE2	GLN- 49	3.01	155.76	H-Bond (Protein Donor)	false
C3'	CB	GLU- 64	4.44	0	Hydrophobic	false
C6	CD1	ILE- 65	4.47	0	Hydrophobic	false
C2'	CG1	ILE- 65	4.07	0	Hydrophobic	false
C9A	CG1	ILE- 65	3.81	0	Hydrophobic	false
O2'	OD2	ASP- 68	2.67	175.85	H-Bond (Ligand Donor)	false
C8M	CB	ARG- 70	4.18	0	Hydrophobic	false
O3'	NH1	ARG- 70	3.36	132.99	H-Bond (Protein Donor)	false
C8M	CB	HIS- 71	4.27	0	Hydrophobic	false