scPDB - 4pkw entry

Protein Data Bank Entry:

PDB ID : 4pkw

Resolution :1.750 Å

Experimental Method : X-ray

Deposition Date : 2014-05-15

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Lethal factor
ID:	LEF_BACAN
AC:	P15917
Organism:	Bacillus anthracis
Reign:	Bacteria
TaxID:	1392
EC Number:	3.4.24.83

Chains:

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

Ligand binding site composition:

B-Factor:	22.331
Number of residues:	31
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
0.824	462.375

% Hydrophobic	% Polar
53.28	46.72
According to VolSite

Ligand :

HET Code:	GM6
Formula:	C20H28N4O4
Molecular weight:	388.461 g/mol
DrugBank ID:	DB02255
Buried Surface Area:	59.83 %
Polar Surface area:	123.32 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	5
Rings:	2
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
10.1402	17.8663	25.4446

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
CAR	CB	ASP- 328	4.26	0	Hydrophobic	false
CAX	CB	PHE- 329	3.38	0	Hydrophobic	false
CAW	CG1	VAL- 653	3.55	0	Hydrophobic	false
CAC	CB	SER- 655	3.83	0	Hydrophobic	false
CAS	CB	SER- 655	3.91	0	Hydrophobic	false
OAL	N	LYS- 656	2.77	143.24	H-Bond (Protein Donor)	false
CAH	CB	LYS- 656	4.45	0	Hydrophobic	false
CAI	CG	LYS- 656	4.12	0	Hydrophobic	false
NAF	O	GLY- 657	2.88	173.17	H-Bond (Ligand Donor)	false
OAZ	N	VAL- 675	3.25	168.93	H-Bond (Protein Donor)	false
CAI	CD1	LEU- 677	3.73	0	Hydrophobic	false
CAI	CB	HIS- 686	4.36	0	Hydrophobic	false
OAG	OE2	GLU- 687	2.51	162.6	H-Bond (Protein Donor)	false
OAE	OH	TYR- 728	2.62	139.33	H-Bond (Protein Donor)	false
CAJ	CD2	TYR- 728	4.1	0	Hydrophobic	false
CAB	CZ	TYR- 728	3.92	0	Hydrophobic	false
OAG	ZN	ZN- 801	2.07	0	Metal Acceptor	false
OAE	ZN	ZN- 801	2.1	0	Metal Acceptor	false