scPDB - 4imf entry

Protein Data Bank Entry:

PDB ID : 4imf

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2013-01-02

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	N-acetylneuraminate lyase
ID:	NANA_PASMU
AC:	Q9CKB0
Organism:	Pasteurella multocida
Reign:	Bacteria
TaxID:	272843
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	94 %
B	6 %

Ligand binding site composition:

B-Factor:	32.766
Number of residues:	33
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.937	722.250

% Hydrophobic	% Polar
48.60	51.40
According to VolSite

Ligand :

HET Code:	SI3
Formula:	C11H18NO9
Molecular weight:	308.262 g/mol
DrugBank ID:	DB11797
Buried Surface Area:	79.93 %
Polar Surface area:	187.45 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	6
Rings:	0
Aromatic rings:	0
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
27.4008	27.2432	21.2561

Binding mode :

What is Poseview ?

2D View
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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
C3	CB	ALA- 10	3.77	0	Hydrophobic	false
C11	CB	SER- 47	3.9	0	Hydrophobic	false
O1A	N	THR- 48	3.17	166.3	H-Bond (Protein Donor)	false
O2	OH	TYR- 136	2.53	146.32	H-Bond (Protein Donor)	false
C11	CD1	ILE- 138	3.54	0	Hydrophobic	false
C11	CZ	PHE- 140	3.98	0	Hydrophobic	false
C11	CD1	LEU- 141	4.18	0	Hydrophobic	false
O4	OG1	THR- 166	2.89	177.26	H-Bond (Protein Donor)	false
O4	O	GLY- 188	2.71	158.57	H-Bond (Ligand Donor)	false
O6	OD1	ASP- 190	2.68	140.3	H-Bond (Ligand Donor)	false
O8	N	ASP- 190	3.05	150.88	H-Bond (Protein Donor)	false
O8	OE1	GLU- 191	2.53	166.63	H-Bond (Ligand Donor)	false
O9	OE2	GLU- 191	3.05	149.3	H-Bond (Ligand Donor)	false
C3	CG2	ILE- 205	3.95	0	Hydrophobic	false
O6	N	SER- 207	2.96	169.25	H-Bond (Protein Donor)	false
O7	OG	SER- 207	2.68	170.17	H-Bond (Protein Donor)	false
C7	CB	SER- 207	4.47	0	Hydrophobic	false
C9	CG2	ILE- 242	4.42	0	Hydrophobic	false
C9	CD2	LEU- 246	4.16	0	Hydrophobic	false
C9	CD1	LEU- 250	4.46	0	Hydrophobic	false
O10	OH	TYR- 251	2.75	162.41	H-Bond (Protein Donor)	false