scPDB - 4fdn entry

Protein Data Bank Entry:

PDB ID : 4fdn

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 2012-05-29

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Decaprenylphosphoryl-beta-D-ribose oxidase
ID:	DPRE1_MYCTU
AC:	P9WJF1
Organism:	Mycobacterium tuberculosis
Reign:	Bacteria
TaxID:	83332
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	27.377
Number of residues:	61
Including
Standard Amino Acids:	56
Non Standard Amino Acids:	1
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.331	759.375

% Hydrophobic	% Polar
49.33	50.67
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	82.57 %
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
39.0285	3.01068	4.82555

Binding mode :

What is Poseview ?

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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
C8M	CE2	TRP- 16	3.88	0	Hydrophobic	false
O2B	O	ALA- 53	2.7	150.39	H-Bond (Ligand Donor)	false
O1A	N	GLY- 55	2.61	139.39	H-Bond (Protein Donor)	false
O1P	N	LEU- 56	3.08	167.37	H-Bond (Protein Donor)	false
O1A	N	GLY- 57	2.92	145.22	H-Bond (Protein Donor)	false
C9	CB	ARG- 58	4.22	0	Hydrophobic	false
C5'	CB	ARG- 58	3.9	0	Hydrophobic	false
C8M	CG	ARG- 58	3.72	0	Hydrophobic	false
O2P	N	ARG- 58	2.72	168.67	H-Bond (Protein Donor)	false
O2A	N	SER- 59	2.85	158.76	H-Bond (Protein Donor)	false
C5B	CB	SER- 59	3.81	0	Hydrophobic	false
C3'	CB	SER- 59	4.49	0	Hydrophobic	false
C8M	CE2	TYR- 60	3.63	0	Hydrophobic	false
C3B	CB	ASN- 63	3.97	0	Hydrophobic	false
C5B	CB	ALA- 64	4.26	0	Hydrophobic	false
C3B	CB	ALA- 64	3.85	0	Hydrophobic	false
O4	N	GLY- 117	2.81	147.51	H-Bond (Protein Donor)	false
N5	N	GLY- 117	3.24	131.74	H-Bond (Protein Donor)	false
C7	CG2	THR- 118	3.52	0	Hydrophobic	false
C8	CG2	THR- 118	3.8	0	Hydrophobic	false
C8	CG2	THR- 118	3.8	0	Hydrophobic	false
C2'	CG1	VAL- 121	4.22	0	Hydrophobic	false
C5'	CG1	VAL- 121	3.9	0	Hydrophobic	false
O1P	N	THR- 122	2.89	163.57	H-Bond (Protein Donor)	false
O1P	OG1	THR- 122	2.67	173.46	H-Bond (Protein Donor)	false
C4B	CB	ALA- 128	4.3	0	Hydrophobic	false
C1B	CB	ALA- 128	3.4	0	Hydrophobic	false
C4B	SG	CYS- 129	3.91	0	Hydrophobic	false
C3'	CB	CYS- 129	4.36	0	Hydrophobic	false
C3'	CG2	ILE- 131	3.94	0	Hydrophobic	false
O2	N	HIS- 132	2.91	163.63	H-Bond (Protein Donor)	false
N3	O	HIS- 132	2.79	137.21	H-Bond (Ligand Donor)	false
O3B	O	ASN- 178	2.93	124.69	H-Bond (Ligand Donor)	false
N6A	O	ILE- 184	3.01	169.13	H-Bond (Ligand Donor)	false
N1A	N	ILE- 184	2.86	153.86	H-Bond (Protein Donor)	false
O2	OH	TYR- 415	2.73	137.31	H-Bond (Protein Donor)	false
C1'	CB	ALA- 417	4.02	0	Hydrophobic	false
C3'	CB	ALA- 417	4.04	0	Hydrophobic	false