scPDB - 4d04 entry

Protein Data Bank Entry:

PDB ID : 4d04

Resolution :1.750 Å

Experimental Method : X-ray

Deposition Date : 2014-04-24

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Phenylacetone monooxygenase
ID:	PAMO_THEFY
AC:	Q47PU3
Organism:	Thermobifida fusca
Reign:	Bacteria
TaxID:	269800
EC Number:	1.14.13.92

Chains:

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

Ligand binding site composition:

B-Factor:	22.667
Number of residues:	61
Including
Standard Amino Acids:	57
Non Standard Amino Acids:	1
Water Molecules:	3
Cofactors:	NAP
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.343	847.125

% Hydrophobic	% Polar
52.19	47.81
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	75.94 %
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
95.8893	73.8253	34.7936

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'	CD2	PHE- 26	4.31	0	Hydrophobic	false
O1P	N	SER- 27	2.88	161.93	H-Bond (Protein Donor)	false
O2P	OG	SER- 27	2.66	175.15	H-Bond (Protein Donor)	false
O3B	OE2	GLU- 46	2.88	131.9	H-Bond (Ligand Donor)	false
O3B	OE1	GLU- 46	2.68	159.35	H-Bond (Ligand Donor)	false
O2B	OE2	GLU- 46	2.66	172.81	H-Bond (Ligand Donor)	false
N3A	N	THR- 47	3.22	152.92	H-Bond (Protein Donor)	false
N3A	OG1	THR- 47	3.33	161.45	H-Bond (Protein Donor)	false
O2A	N	VAL- 54	2.78	164.99	H-Bond (Protein Donor)	false
C8M	CG1	VAL- 54	3.84	0	Hydrophobic	false
C9	CG1	VAL- 54	3.93	0	Hydrophobic	false
C9A	CG2	VAL- 54	4.35	0	Hydrophobic	false
C2'	CG1	VAL- 54	3.98	0	Hydrophobic	false
C5'	CG1	VAL- 54	4.43	0	Hydrophobic	false
C8	CG2	VAL- 54	3.99	0	Hydrophobic	false
O3B	NE1	TRP- 57	3.36	148.77	H-Bond (Protein Donor)	false
O2B	NE1	TRP- 57	3.1	143.36	H-Bond (Protein Donor)	false
C7M	CB	ASN- 58	3.81	0	Hydrophobic	false
C7M	CE2	TYR- 60	4.46	0	Hydrophobic	false
O4	N	ASP- 66	2.77	167.83	H-Bond (Protein Donor)	false
O3'	OH	TYR- 72	2.7	161.12	H-Bond (Protein Donor)	false
N6A	O	VAL- 119	2.93	157.5	H-Bond (Ligand Donor)	false
N1A	N	VAL- 119	2.87	168.65	H-Bond (Protein Donor)	false
O2'	OE1	GLN- 152	2.81	148.21	H-Bond (Ligand Donor)	false
O2P	NE2	GLN- 152	3.19	158.49	H-Bond (Protein Donor)	false
C8M	CB	LEU- 153	3.84	0	Hydrophobic	false
C1'	CD1	LEU- 153	4.12	0	Hydrophobic	false
C9	CD1	LEU- 153	3.87	0	Hydrophobic	false
C8M	CZ	PHE- 389	4	0	Hydrophobic	false
O2	N	MET- 446	2.85	160.55	H-Bond (Protein Donor)	false
C3'	CB	MET- 446	3.77	0	Hydrophobic	false
C1'	SD	MET- 446	3.85	0	Hydrophobic	false
C4'	CD1	ILE- 450	3.88	0	Hydrophobic	false
N5	N7N	NAP- 701	2.78	170.08	H-Bond (Protein Donor)	false
C7M	C5N	NAP- 701	3.49	0	Hydrophobic	false
O1P	O	HOH- 2010	2.55	176.09	H-Bond (Protein Donor)	false
O2P	O	HOH- 2108	2.74	172.16	H-Bond (Protein Donor)	false