scPDB - 3m6p entry

Protein Data Bank Entry:

PDB ID : 3m6p

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2010-03-16

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Peptide deformylase 1B, chloroplastic/mitochondrial
ID:	DEF1B_ARATH
AC:	Q9FUZ2
Organism:	Arabidopsis thaliana
Reign:	Eukaryota
TaxID:	3702
EC Number:	3.5.1.88

Chains:

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

Ligand binding site composition:

B-Factor:	20.136
Number of residues:	29
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
0.563	364.500

% Hydrophobic	% Polar
47.22	52.78
According to VolSite

Ligand :

HET Code:	BB2
Formula:	C19H35N3O5
Molecular weight:	385.498 g/mol
DrugBank ID:	DB04310
Buried Surface Area:	67.18 %
Polar Surface area:	118.97 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	4
Rings:	1
Aromatic rings:	0
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
16.3359	8.08004	24.2004

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
O13	N	ILE- 42	2.84	154.64	H-Bond (Protein Donor)	false
C11	CD1	ILE- 42	3.87	0	Hydrophobic	false
C8	CG1	ILE- 42	3.95	0	Hydrophobic	false
C9	CD1	ILE- 42	3.86	0	Hydrophobic	false
C24	CD1	ILE- 42	3.76	0	Hydrophobic	false
N1	O	GLY- 43	3.4	124.48	H-Bond (Ligand Donor)	false
O4	NE2	GLN- 48	3.22	173.03	H-Bond (Protein Donor)	false
C11	CE2	PHE- 87	3.75	0	Hydrophobic	false
C25	CZ	PHE- 87	4.41	0	Hydrophobic	false
O27	O	ASP- 88	2.59	163.98	H-Bond (Ligand Donor)	false
C11	CB	GLU- 89	4.47	0	Hydrophobic	false
N14	O	GLY- 90	3.22	169.08	H-Bond (Ligand Donor)	false
O20	N	GLY- 90	2.98	160.31	H-Bond (Protein Donor)	false
C5	CG	LEU- 92	3.87	0	Hydrophobic	false
C18	CD2	LEU- 92	4.11	0	Hydrophobic	false
O4	N	LEU- 92	3	155.2	H-Bond (Protein Donor)	false
C17	CE2	TYR- 98	3.25	0	Hydrophobic	false
C10	CG	ARG- 129	4.26	0	Hydrophobic	false
C9	CG1	ILE- 130	3.91	0	Hydrophobic	false
C9	CB	HIS- 133	3.95	0	Hydrophobic	false
O4	ZN	ZN- 195	2.1	0	Metal Acceptor	false
O2	ZN	ZN- 195	2.37	0	Metal Acceptor	false