scPDB - 4iv6 entry

Protein Data Bank Entry:

PDB ID : 4iv6

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2013-01-22

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Isovaleryl-CoA dehydrogenase
ID:	A0QTW7_MYCS2
AC:	A0QTW7
Organism:	Mycobacterium smegmatis 155)
Reign:	Bacteria
TaxID:	246196
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	61 %
B	39 %

Ligand binding site composition:

B-Factor:	16.535
Number of residues:	58
Including
Standard Amino Acids:	54
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.191	1495.125

% Hydrophobic	% Polar
50.79	49.21
According to VolSite

Ligand :

HET Code:	FDA
Formula:	C27H33N9O15P2
Molecular weight:	785.550 g/mol
DrugBank ID:	-
Buried Surface Area:	74.3 %
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
51.4881	39.2447	29.5837

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	MET- 120	2.93	174.19	H-Bond (Ligand Donor)	false
O2	N	LEU- 122	2.92	152.97	H-Bond (Protein Donor)	false
N1	OG1	THR- 123	2.84	176.66	H-Bond (Protein Donor)	false
O2	N	THR- 123	3	173.97	H-Bond (Protein Donor)	false
O2	OG1	THR- 123	3.22	122.69	H-Bond (Protein Donor)	false
C1'	CB	THR- 123	3.94	0	Hydrophobic	false
C3'	CG2	THR- 123	4.35	0	Hydrophobic	false
O2P	N	GLY- 128	2.71	148.07	H-Bond (Protein Donor)	false
O2A	N	SER- 129	3.48	131.79	H-Bond (Protein Donor)	false
O2A	OG	SER- 129	2.63	144.75	H-Bond (Protein Donor)	false
C7M	CE3	TRP- 153	3.89	0	Hydrophobic	false
C8M	CD2	TRP- 153	3.72	0	Hydrophobic	false
C1'	CB	TRP- 153	3.77	0	Hydrophobic	false
C9	CB	TRP- 153	3.58	0	Hydrophobic	false
O4	N	SER- 155	2.96	162.76	H-Bond (Protein Donor)	false
N5	OG	SER- 155	2.96	163.3	H-Bond (Protein Donor)	false
C7M	CD	LYS- 199	3.41	0	Hydrophobic	false
C7M	CD2	TYR- 202	3.75	0	Hydrophobic	false
C6	CB	SER- 207	4.43	0	Hydrophobic	false
C7M	CB	SER- 207	4.42	0	Hydrophobic	false
O1A	NH2	ARG- 267	3.27	133.89	H-Bond (Protein Donor)	false
O1A	NE	ARG- 267	2.77	165.4	H-Bond (Protein Donor)	false
O2P	NH2	ARG- 267	2.94	136.39	H-Bond (Protein Donor)	false
O1A	CZ	ARG- 267	3.45	0	Ionic (Protein Cationic)	false
N7A	OG	SER- 269	2.81	150.76	H-Bond (Protein Donor)	false
C4B	CD1	ILE- 274	3.76	0	Hydrophobic	false
C4B	CG2	VAL- 280	4.49	0	Hydrophobic	false
C1B	CG2	VAL- 280	3.61	0	Hydrophobic	false
O3B	O	ARG- 335	2.72	170.77	H-Bond (Ligand Donor)	false
O1P	N	GLY- 339	2.76	155.39	H-Bond (Protein Donor)	false
C7M	CD2	TYR- 342	4.03	0	Hydrophobic	false
C8M	CB	TYR- 342	4.03	0	Hydrophobic	false
C8	CD2	LEU- 357	3.5	0	Hydrophobic	false
O2'	N	GLY- 363	3.39	167.91	H-Bond (Protein Donor)	false
O2B	OG1	THR- 364	2.71	155.99	H-Bond (Protein Donor)	false
C2B	CG2	THR- 364	3.89	0	Hydrophobic	false
C5'	CG2	THR- 364	3.51	0	Hydrophobic	false
O2B	OE1	GLU- 366	2.64	137.91	H-Bond (Ligand Donor)	false
N1A	ND2	ASN- 370	3.32	144.35	H-Bond (Protein Donor)	false
O4'	O	HOH- 535	3.25	169.49	H-Bond (Ligand Donor)	false
O2A	O	HOH- 607	2.73	179.95	H-Bond (Protein Donor)	false