scPDB - 3oib entry

Protein Data Bank Entry:

PDB ID : 3oib

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2010-08-18

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Putative acyl-CoA dehydrogenase
ID:	A0R3J1_MYCS2
AC:	A0R3J1
Organism:	Mycobacterium smegmatis 155)
Reign:	Bacteria
TaxID:	246196
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	64 %
B	36 %

Ligand binding site composition:

B-Factor:	14.661
Number of residues:	61
Including
Standard Amino Acids:	56
Non Standard Amino Acids:	0
Water Molecules:	5
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.104	580.500

% Hydrophobic	% Polar
48.84	51.16
According to VolSite

Ligand :

HET Code:	FDA
Formula:	C27H33N9O15P2
Molecular weight:	785.550 g/mol
DrugBank ID:	-
Buried Surface Area:	67.38 %
Polar Surface area:	381.04 Å2

Number of
H-Bond Acceptors:	21
H-Bond Donors:	9
Rings:	6
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
-1.09713	28.7856	48.8455

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
N3	O	LEU- 145	2.88	173.1	H-Bond (Ligand Donor)	false
O2	N	ILE- 147	2.97	157.93	H-Bond (Protein Donor)	false
N1	OG1	THR- 148	2.89	169.51	H-Bond (Protein Donor)	false
O2	OG1	THR- 148	3.23	122.64	H-Bond (Protein Donor)	false
O2	N	THR- 148	2.98	165.71	H-Bond (Protein Donor)	false
C1'	CB	THR- 148	4.01	0	Hydrophobic	false
C3'	CG2	THR- 148	4.31	0	Hydrophobic	false
O1P	N	GLY- 153	2.77	125.98	H-Bond (Protein Donor)	false
O1A	OG	SER- 154	2.84	142.92	H-Bond (Protein Donor)	false
O1A	N	SER- 154	3.22	147.52	H-Bond (Protein Donor)	false
C8A	CB	SER- 154	4.43	0	Hydrophobic	false
C1'	CB	TYR- 178	3.61	0	Hydrophobic	false
C9	CB	TYR- 178	3.39	0	Hydrophobic	false
O4	OG1	THR- 180	3.34	128.1	H-Bond (Protein Donor)	false
O4	N	THR- 180	2.8	157.54	H-Bond (Protein Donor)	false
N5	OG1	THR- 180	2.71	134.46	H-Bond (Protein Donor)	false
C7M	CD	LYS- 222	3.42	0	Hydrophobic	false
C7M	CE3	TRP- 225	4.1	0	Hydrophobic	false
C7M	CG2	THR- 230	4.24	0	Hydrophobic	false
O2A	NE	ARG- 289	2.88	150.59	H-Bond (Protein Donor)	false
O2A	NH2	ARG- 289	2.96	143.14	H-Bond (Protein Donor)	false
O1P	NH2	ARG- 289	3.15	124.66	H-Bond (Protein Donor)	false
O2A	CZ	ARG- 289	3.35	0	Ionic (Protein Cationic)	false
C8A	CG2	THR- 291	3.92	0	Hydrophobic	false
C1B	CD2	LEU- 296	4.09	0	Hydrophobic	false
C8A	CD2	LEU- 296	3.66	0	Hydrophobic	false
C5A	CD2	LEU- 296	4.02	0	Hydrophobic	false
C5B	CD1	LEU- 296	4.07	0	Hydrophobic	false
C7M	CD2	TYR- 365	4.44	0	Hydrophobic	false
C8M	CD2	TYR- 365	4.25	0	Hydrophobic	false
C8M	CE	MET- 366	4	0	Hydrophobic	false
C7	CD1	ILE- 380	3.36	0	Hydrophobic	false
C7M	CD1	ILE- 380	3.74	0	Hydrophobic	false
C5'	CG2	ILE- 383	4.34	0	Hydrophobic	false
O2B	OG1	THR- 387	2.75	159.66	H-Bond (Protein Donor)	false
C2B	CG2	THR- 387	3.87	0	Hydrophobic	false
C5'	CG2	THR- 387	3.61	0	Hydrophobic	false
O2B	OE1	GLU- 389	3.3	125.85	H-Bond (Ligand Donor)	false
C8A	CD1	ILE- 390	4.49	0	Hydrophobic	false
O4	O	HOH- 610	2.92	179.97	H-Bond (Protein Donor)	false
O4'	O	HOH- 699	2.64	179.96	H-Bond (Protein Donor)	false
O2P	O	HOH- 747	2.78	179.98	H-Bond (Protein Donor)	false