scPDB - 2ivf entry

Protein Data Bank Entry:

PDB ID : 2ivf

Resolution :1.880 Å

Experimental Method : X-ray

Deposition Date : 2006-06-13

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Alpha-subunit of ethylbenzene dehydrogenase
ID:	Q5P5I0_AROAE
AC:	Q5P5I0
Organism:	Aromatoleum aromaticum
Reign:	Bacteria
TaxID:	76114
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	23.867
Number of residues:	71
Including
Standard Amino Acids:	66
Non Standard Amino Acids:	1
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.615	513.000

% Hydrophobic	% Polar
44.74	55.26
According to VolSite

Ligand :

HET Code:	MGD
Formula:	C20H24N10O13P2S2
Molecular weight:	738.541 g/mol
DrugBank ID:	-
Buried Surface Area:	81.31 %
Polar Surface area:	440.93 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	10
Rings:	6
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
29.6139	26.6946	9.40809

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
C11	CB	TRP- 87	4.32	0	Hydrophobic	false
C23	CB	TRP- 87	3.5	0	Hydrophobic	false
N3	N	CYS- 254	3.39	123.19	H-Bond (Protein Donor)	false
O1A	N	ASN- 256	2.93	147.09	H-Bond (Protein Donor)	false
C5'	CB	ASN- 256	3.76	0	Hydrophobic	false
N19	O	TYR- 259	2.83	131.88	H-Bond (Ligand Donor)	false
O1A	OG1	THR- 260	2.81	165.96	H-Bond (Protein Donor)	false
C10	CG2	THR- 260	4.21	0	Hydrophobic	false
C11	CB	THR- 260	4.37	0	Hydrophobic	false
C23	CB	THR- 260	4.16	0	Hydrophobic	false
N22	O	THR- 260	3.01	138.46	H-Bond (Ligand Donor)	false
N2	O	ILE- 281	2.83	153.25	H-Bond (Ligand Donor)	false
O2'	OD1	ASP- 284	2.66	154.39	H-Bond (Ligand Donor)	false
O3'	ND2	ASN- 286	3	141.31	H-Bond (Protein Donor)	false
O6	N	GLY- 301	2.78	157.86	H-Bond (Protein Donor)	false
N1	OD2	ASP- 303	3.42	123.54	H-Bond (Ligand Donor)	false
N1	OD1	ASP- 303	2.81	176.3	H-Bond (Ligand Donor)	false
N2	OD2	ASP- 303	2.64	145.4	H-Bond (Ligand Donor)	false
O2A	N	PHE- 446	2.89	155.37	H-Bond (Protein Donor)	false
C10	CD2	PHE- 446	4.48	0	Hydrophobic	false
O2B	OG	SER- 447	2.7	154.18	H-Bond (Protein Donor)	false
O5'	OG	SER- 447	3.38	120.42	H-Bond (Protein Donor)	false
C1'	CB	SER- 447	4.38	0	Hydrophobic	false
O1B	N	HIS- 849	2.89	164.81	H-Bond (Protein Donor)	false
C10	CB	HIS- 849	4.05	0	Hydrophobic	false
N18	O	SER- 853	2.83	154.55	H-Bond (Ligand Donor)	false
O17	N	HIS- 855	2.73	168.18	H-Bond (Protein Donor)	false
O2B	NH2	ARG- 967	2.85	152.49	H-Bond (Protein Donor)	false
O2B	CZ	ARG- 967	3.93	0	Ionic (Protein Cationic)	false
O3'	O	HOH- 2102	2.74	152.98	H-Bond (Ligand Donor)	false
O1B	O	HOH- 2412	2.81	158.44	H-Bond (Protein Donor)	false