scPDB - 5fv0 entry

Protein Data Bank Entry:

PDB ID : 5fv0

Resolution :2.910 Å

Experimental Method : X-ray

Deposition Date : 2016-02-01

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	ESX secretion system protein EccC
ID:	A4IKE7_GEOTN
AC:	A4IKE7
Organism:	Geobacillus thermodenitrificans
Reign:	Bacteria
TaxID:	420246
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	55.626
Number of residues:	34
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.432	266.625

% Hydrophobic	% Polar
46.84	53.16
According to VolSite

Ligand :

HET Code:	ONA
Formula:	C18H19N6O14P3
Molecular weight:	636.297 g/mol
DrugBank ID:	-
Buried Surface Area:	41.91 %
Polar Surface area:	337.98 Å2

Number of
H-Bond Acceptors:	19
H-Bond Donors:	3
Rings:	4
Aromatic rings:	3
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	12

Mass center Coordinates

X	Y	Z
39.8993	52.9027	41.0543

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
O3B	N	GLY- 1004	3.38	120.19	H-Bond (Protein Donor)	false
O2B	N	GLY- 1004	3.03	146.64	H-Bond (Protein Donor)	false
O3B	N	TYR- 1005	3.27	160.43	H-Bond (Protein Donor)	false
O5'	N	GLY- 1006	2.79	136.12	H-Bond (Protein Donor)	false
O3B	N	GLY- 1006	3.38	120.72	H-Bond (Protein Donor)	false
O1A	N	LYS- 1007	3.12	130.43	H-Bond (Protein Donor)	false
O3B	N	LYS- 1007	3.22	160.19	H-Bond (Protein Donor)	false
O3B	NZ	LYS- 1007	3.23	159.99	H-Bond (Protein Donor)	false
O3B	NZ	LYS- 1007	3.23	0	Ionic (Protein Cationic)	false
O1A	N	SER- 1008	3.17	167.53	H-Bond (Protein Donor)	false
CA4	CG2	THR- 1009	4.48	0	Hydrophobic	false
C1'	CB	THR- 1009	4.4	0	Hydrophobic	false
O3A	N	THR- 1009	3.19	133.91	H-Bond (Protein Donor)	false
O3A	OG1	THR- 1009	2.6	151.93	H-Bond (Protein Donor)	false
CA7	CB	ALA- 1038	4.04	0	Hydrophobic	false
N6	O	ILE- 1197	3.12	126.07	H-Bond (Ligand Donor)	false
CA2	CB	ASP- 1206	3.97	0	Hydrophobic	false
CA4	CG1	VAL- 1209	4.08	0	Hydrophobic	false
O3G	O	HOH- 2006	2.92	157.36	H-Bond (Protein Donor)	false