scPDB - 3lov entry

Protein Data Bank Entry:

PDB ID : 3lov

Resolution :2.060 Å

Experimental Method : X-ray

Deposition Date : 2010-02-04

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Protoporphyrinogen oxidase
ID:	B1YKJ9_EXIS2
AC:	B1YKJ9
Organism:	Exiguobacterium sibiricum
Reign:	Bacteria
TaxID:	262543
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	22.366
Number of residues:	64
Including
Standard Amino Acids:	60
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.830	519.750

% Hydrophobic	% Polar
49.35	50.65
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	70.68 %
Polar Surface area:	381.7 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	7
Rings:	6
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
26.3788	25.1707	87.7306

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
C4'	CG2	ILE- 13	3.96	0	Hydrophobic	false
O1P	OG1	THR- 14	2.71	164.77	H-Bond (Protein Donor)	false
O2P	OG1	THR- 14	3.33	127.2	H-Bond (Protein Donor)	false
O2P	N	THR- 14	3.26	160.29	H-Bond (Protein Donor)	false
O3B	OE1	GLU- 35	2.51	163.51	H-Bond (Ligand Donor)	false
O2B	OE2	GLU- 35	2.55	155.44	H-Bond (Ligand Donor)	false
O2B	OE1	GLU- 35	3.45	147.02	H-Bond (Ligand Donor)	false
N3A	N	ALA- 36	3.23	136.81	H-Bond (Protein Donor)	false
O1A	N	LYS- 43	2.86	167.84	H-Bond (Protein Donor)	false
O2A	NZ	LYS- 43	2.88	159.93	H-Bond (Protein Donor)	false
O2A	NZ	LYS- 43	2.88	0	Ionic (Protein Cationic)	false
C8M	CD	LYS- 43	4.25	0	Hydrophobic	false
C9	CD	LYS- 43	4.45	0	Hydrophobic	false
C5'	CD	LYS- 43	4.49	0	Hydrophobic	false
C9A	CG	PRO- 58	4.15	0	Hydrophobic	false
C2'	CG	PRO- 58	3.88	0	Hydrophobic	false
N3	O	SER- 60	2.66	127.5	H-Bond (Ligand Donor)	false
C6	CD1	ILE- 173	4.28	0	Hydrophobic	false
N6A	O	LEU- 256	3.26	166.87	H-Bond (Ligand Donor)	false
N1A	N	LEU- 256	3.06	173.65	H-Bond (Protein Donor)	false
C1B	CG2	ILE- 284	4.39	0	Hydrophobic	false
N7A	NE2	GLN- 288	2.86	137.22	H-Bond (Protein Donor)	false
N6A	OE1	GLN- 288	2.77	158.8	H-Bond (Ligand Donor)	false
C7M	CB	THR- 309	3.63	0	Hydrophobic	false
C7M	CD1	LEU- 405	4.02	0	Hydrophobic	false
C8M	CD2	LEU- 405	3.95	0	Hydrophobic	false
C8M	CG	LEU- 409	3.59	0	Hydrophobic	false
C7	CD1	LEU- 409	4.45	0	Hydrophobic	false
C9	CD2	LEU- 409	3.73	0	Hydrophobic	false
C3'	CD1	LEU- 439	4.3	0	Hydrophobic	false
C5'	CB	LEU- 439	4.11	0	Hydrophobic	false
C1'	CG1	VAL- 444	3.88	0	Hydrophobic	false
O3'	O	VAL- 444	2.55	164.96	H-Bond (Ligand Donor)	false
O2	N	LEU- 446	2.8	166.06	H-Bond (Protein Donor)	false
C4'	CD2	LEU- 446	3.84	0	Hydrophobic	false
C2'	CD2	LEU- 446	4.08	0	Hydrophobic	false
C5'	SG	CYS- 449	3.73	0	Hydrophobic	false
O2P	O	HOH- 484	2.67	179.98	H-Bond (Protein Donor)	false
O3B	O	HOH- 487	2.64	179.96	H-Bond (Protein Donor)	false