scPDB - 2dki entry

Protein Data Bank Entry:

PDB ID : 2dki

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2006-04-11

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	3-hydroxybenzoate 4-monooxygenase
ID:	MOBA_COMTE
AC:	Q6SSJ6
Organism:	Comamonas testosteroni
Reign:	Bacteria
TaxID:	285
EC Number:	1.14.13.23

Chains:

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

Ligand binding site composition:

B-Factor:	33.621
Number of residues:	52
Including
Standard Amino Acids:	52
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.234	570.375

% Hydrophobic	% Polar
39.64	60.36
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	61.81 %
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
10.8452	42.3221	22.2402

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'	CG	PRO- 42	4.5	0	Hydrophobic	false
O1P	N	ALA- 43	2.79	162.28	H-Bond (Protein Donor)	false
O3B	OE2	GLU- 63	2.58	165.43	H-Bond (Ligand Donor)	false
O2B	OE1	GLU- 63	2.56	162.54	H-Bond (Ligand Donor)	false
O2B	OE2	GLU- 63	3.5	137.58	H-Bond (Ligand Donor)	false
O2B	NE2	GLN- 64	3.28	162.1	H-Bond (Protein Donor)	false
N3A	N	GLN- 64	3.16	136.18	H-Bond (Protein Donor)	false
C6	CB	GLN- 73	3.91	0	Hydrophobic	false
C2'	CG	GLN- 73	4.26	0	Hydrophobic	false
C9A	CG	GLN- 73	3.77	0	Hydrophobic	false
C2'	CB	ALA- 74	4.22	0	Hydrophobic	false
N6A	O	VAL- 166	3.28	159.79	H-Bond (Ligand Donor)	false
N1A	N	VAL- 166	2.87	156.82	H-Bond (Protein Donor)	false
C1B	CB	ASP- 207	4.49	0	Hydrophobic	false
N3	OH	TYR- 271	2.99	146.9	H-Bond (Ligand Donor)	false
C7M	CB	SER- 315	4.4	0	Hydrophobic	false
C6	CB	TYR- 317	4.41	0	Hydrophobic	false
C1'	CE2	TYR- 317	4.03	0	Hydrophobic	false
O3'	OD2	ASP- 349	3.1	134.16	H-Bond (Ligand Donor)	false
O2P	N	ASP- 349	2.89	166.45	H-Bond (Protein Donor)	false
C4'	CB	MET- 362	4.19	0	Hydrophobic	false
O2P	OG	SER- 365	3	159.65	H-Bond (Protein Donor)	false