scPDB - 2yxl entry

Protein Data Bank Entry:

PDB ID : 2yxl

Resolution :2.550 Å

Experimental Method : X-ray

Deposition Date : 2007-04-26

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	450aa long hypothetical fmu protein
ID:	O58581_PYRHO
AC:	O58581
Organism:	Pyrococcus horikoshii
Reign:	Archaea
TaxID:	70601
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	32.962
Number of residues:	30
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.216	2531.250

% Hydrophobic	% Polar
50.13	49.87
According to VolSite

Ligand :

HET Code:	SFG
Formula:	C15H24N7O5
Molecular weight:	382.395 g/mol
DrugBank ID:	DB01910
Buried Surface Area:	67.2 %
Polar Surface area:	214.71 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	5
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	2
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
-18.9799	80.0734	21.0297

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
N	O	ALA- 267	2.95	178.41	H-Bond (Ligand Donor)	false
C4'	CB	ALA- 267	4.12	0	Hydrophobic	false
C1'	CB	ALA- 267	4.21	0	Hydrophobic	false
O	N	GLY- 271	3.07	143.95	H-Bond (Protein Donor)	false
O	N	GLY- 272	2.9	150.23	H-Bond (Protein Donor)	false
OXT	NZ	LYS- 273	3.38	160.93	H-Bond (Protein Donor)	false
OXT	N	LYS- 273	3.24	140.29	H-Bond (Protein Donor)	false
OXT	NZ	LYS- 273	3.38	0	Ionic (Protein Cationic)	false
O3'	OD1	ASP- 291	2.79	169.92	H-Bond (Ligand Donor)	false
O3'	OD2	ASP- 291	3.44	134.04	H-Bond (Ligand Donor)	false
O2'	OD2	ASP- 291	2.83	156.15	H-Bond (Ligand Donor)	false
N3	N	VAL- 292	3.34	146.88	H-Bond (Protein Donor)	false
N6	OD1	ASP- 318	3.37	170.65	H-Bond (Ligand Donor)	false
N1	N	ALA- 319	3.06	148.01	H-Bond (Protein Donor)	false
N	OD2	ASP- 337	2.71	169.74	H-Bond (Ligand Donor)	false
N	OD2	ASP- 337	2.71	0	Ionic (Ligand Cationic)	false
NE	OD2	ASP- 337	3.95	0	Ionic (Ligand Cationic)	false
C5'	CB	PRO- 339	4.17	0	Hydrophobic	false