scPDB - 3up4 entry

Protein Data Bank Entry:

PDB ID : 3up4

Resolution :2.800 Å

Experimental Method : X-ray

Deposition Date : 2011-11-17

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase
ID:	OTEMO_PSEPU
AC:	H3JQW0
Organism:	Pseudomonas putida
Reign:	Bacteria
TaxID:	303
EC Number:	1.14.13.160

Chains:

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

Ligand binding site composition:

B-Factor:	29.093
Number of residues:	56
Including
Standard Amino Acids:	55
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:	NAP
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.469	617.625

% Hydrophobic	% Polar
40.44	59.56
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	79 %
Polar Surface area:	381.7 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	7
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
9.73894	-5.68745	-55.9503

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
C4'	CG2	VAL- 19	4.36	0	Hydrophobic	false
O1P	N	THR- 20	2.98	153.44	H-Bond (Protein Donor)	false
O2P	OG1	THR- 20	2.7	147.52	H-Bond (Protein Donor)	false
O3B	OE2	GLU- 39	3.02	123.63	H-Bond (Ligand Donor)	false
O3B	OE1	GLU- 39	2.58	166.63	H-Bond (Ligand Donor)	false
O2B	OE1	GLU- 39	3.31	150.07	H-Bond (Ligand Donor)	false
N3A	N	ALA- 40	3.2	133.35	H-Bond (Protein Donor)	false
O2A	N	THR- 47	2.83	166.52	H-Bond (Protein Donor)	false
O4'	OG1	THR- 47	2.63	164.25	H-Bond (Protein Donor)	false
O2'	OG1	THR- 47	3.47	137.26	H-Bond (Ligand Donor)	false
C8	CG2	THR- 47	3.45	0	Hydrophobic	false
O3B	NE1	TRP- 50	3.33	136.13	H-Bond (Protein Donor)	false
O2B	NE1	TRP- 50	2.9	157.38	H-Bond (Protein Donor)	false
C7M	CB	ASN- 51	4.23	0	Hydrophobic	false
C7M	CE2	TYR- 53	4.28	0	Hydrophobic	false
O4	N	ASP- 59	2.7	156.01	H-Bond (Protein Donor)	false
N3	OG1	THR- 60	2.95	158.82	H-Bond (Ligand Donor)	false
O3'	OH	TYR- 65	2.88	166.09	H-Bond (Protein Donor)	false
N6A	O	VAL- 112	3.29	154.87	H-Bond (Ligand Donor)	false
N1A	N	VAL- 112	2.98	171.19	H-Bond (Protein Donor)	false
C8M	CB	LEU- 146	4.18	0	Hydrophobic	false
C9	CD1	LEU- 146	4.18	0	Hydrophobic	false
C1'	CD1	LEU- 146	4.35	0	Hydrophobic	false
C8M	CE2	PHE- 389	3.9	0	Hydrophobic	false
O2	N	VAL- 446	2.92	167.31	H-Bond (Protein Donor)	false
C5'	CG1	VAL- 446	3.73	0	Hydrophobic	false
N5	N7N	NAP- 552	3.06	151.37	H-Bond (Protein Donor)	false
C7M	C5N	NAP- 552	3.28	0	Hydrophobic	false