scPDB - 2npf entry

Protein Data Bank Entry:

PDB ID : 2npf

Resolution :2.900 Å

Experimental Method : X-ray

Deposition Date : 2006-10-27

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Elongation factor 2
ID:	EF2_YEAST
AC:	P32324
Organism:	Saccharomyces cerevisiae
Reign:	Eukaryota
TaxID:	559292
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	38.305
Number of residues:	41
Including
Standard Amino Acids:	41
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.201	627.750

% Hydrophobic	% Polar
55.91	44.09
According to VolSite

Ligand :

HET Code:	MOU
Formula:	C37H52O12
Molecular weight:	688.802 g/mol
DrugBank ID:	-
Buried Surface Area:	62.17 %
Polar Surface area:	180.77 Å2

Number of
H-Bond Acceptors:	12
H-Bond Donors:	1
Rings:	6
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	15

Mass center Coordinates

X	Y	Z
2.90057	15.1976	41.902

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
C2	CB	PRO- 487	3.93	0	Hydrophobic	false
C41	CG	GLN- 490	3.62	0	Hydrophobic	false
C43	CG	GLN- 490	4.37	0	Hydrophobic	false
C2	CD2	LEU- 519	3.9	0	Hydrophobic	false
C36	CD2	LEU- 519	4.18	0	Hydrophobic	false
C31	CD2	LEU- 519	4.35	0	Hydrophobic	false
C22	CE1	TYR- 521	4.06	0	Hydrophobic	false
C26	CE1	TYR- 521	3.92	0	Hydrophobic	false
C28	CZ	TYR- 521	3.94	0	Hydrophobic	false
C30	CZ	TYR- 521	3.67	0	Hydrophobic	false
C34	CG	TYR- 521	3.98	0	Hydrophobic	false
C22	CB	SER- 523	4.38	0	Hydrophobic	false
C14	CB	GLU- 524	4.21	0	Hydrophobic	false
O24	N	GLU- 524	2.77	152.25	H-Bond (Protein Donor)	false
O25	N	GLU- 524	3.36	146.49	H-Bond (Protein Donor)	false
C22	CG1	ILE- 529	3.99	0	Hydrophobic	false
C39	CB	ALA- 531	4.49	0	Hydrophobic	false
C21	CB	PRO- 559	4.03	0	Hydrophobic	false
C22	CB	PRO- 559	4.27	0	Hydrophobic	false
C21	CG2	VAL- 561	4.3	0	Hydrophobic	false
O12	N	ALA- 562	2.84	174.15	H-Bond (Protein Donor)	false
C7	CB	PRO- 727	3.52	0	Hydrophobic	false
C6	CE1	PHE- 729	4.17	0	Hydrophobic	false
C32	CE1	PHE- 729	4.39	0	Hydrophobic	false
C21	CG1	VAL- 774	4.14	0	Hydrophobic	false
C7	CG2	VAL- 774	4.12	0	Hydrophobic	false
C43	CB	SER- 777	4.47	0	Hydrophobic	false
C44	CB	PHE- 780	4.4	0	Hydrophobic	false
C44	CG2	THR- 781	3.92	0	Hydrophobic	false
O46	N	THR- 781	3.02	138.88	H-Bond (Protein Donor)	false
C38	CG	MET- 796	4.34	0	Hydrophobic	false
C40	CG	MET- 796	3.62	0	Hydrophobic	false
C6	CB	PHE- 798	4.28	0	Hydrophobic	false
C7	CD1	PHE- 798	4	0	Hydrophobic	false
C13	CB	PHE- 798	3.92	0	Hydrophobic	false
C17	CE2	PHE- 798	3.83	0	Hydrophobic	false
C18	CZ	PHE- 798	4.28	0	Hydrophobic	false
C16	CD2	PHE- 798	3.64	0	Hydrophobic	false
O33	N	PHE- 798	3.21	169.14	H-Bond (Protein Donor)	false
C18	CZ2	TRP- 801	3.46	0	Hydrophobic	false