scPDB - 3r5w entry

Protein Data Bank Entry:

PDB ID : 3r5w

Resolution :1.790 Å

Experimental Method : X-ray

Deposition Date : 2011-03-20

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Deazaflavin-dependent nitroreductase
ID:	DDN_MYCTU
AC:	P9WP15
Organism:	Mycobacterium tuberculosis
Reign:	Bacteria
TaxID:	83332
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
B	24 %
N	76 %

Ligand binding site composition:

B-Factor:	29.267
Number of residues:	44
Including
Standard Amino Acids:	41
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.015	1599.750

% Hydrophobic	% Polar
43.25	56.75
According to VolSite

Ligand :

HET Code:	F42
Formula:	C29H32N5O18P
Molecular weight:	769.561 g/mol
DrugBank ID:	DB03913
Buried Surface Area:	62.48 %
Polar Surface area:	389.68 Å2

Number of
H-Bond Acceptors:	20
H-Bond Donors:	7
Rings:	3
Aromatic rings:	1
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	20

Mass center Coordinates

X	Y	Z
-8.19557	11.8004	-29.197

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
O8M	N	VAL- 46	2.84	165.91	H-Bond (Protein Donor)	false
C6	CG1	VAL- 46	3.82	0	Hydrophobic	false
C7	CG2	VAL- 46	4.25	0	Hydrophobic	false
O6G	NE	ARG- 54	3.3	173.2	H-Bond (Protein Donor)	false
O7G	NE	ARG- 54	2.53	121.96	H-Bond (Protein Donor)	false
O7G	CZ	ARG- 54	3.38	0	Ionic (Protein Cationic)	false
C3G	CG	ARG- 54	4	0	Hydrophobic	false
O2W	N	LYS- 55	3.41	120.01	H-Bond (Protein Donor)	false
C3G	CB	LYS- 55	3.89	0	Hydrophobic	false
O6G	NZ	LYS- 55	3.53	0	Ionic (Protein Cationic)	false
O2W	N	THR- 56	2.99	170.05	H-Bond (Protein Donor)	false
O2W	OG1	THR- 56	3.02	166.9	H-Bond (Protein Donor)	false
C4H	CD	ARG- 60	3.4	0	Hydrophobic	false
O2V	CZ	ARG- 60	3.05	0	Ionic (Protein Cationic)	false
O2'	O	PRO- 63	2.73	176.4	H-Bond (Ligand Donor)	false
C9	CG	PRO- 63	3.71	0	Hydrophobic	false
C2'	CD2	LEU- 64	4.06	0	Hydrophobic	false
O4	N	TYR- 65	3.12	165.37	H-Bond (Protein Donor)	false
N3	O	ALA- 76	2.94	153.87	H-Bond (Ligand Donor)	false
O2	N	LYS- 79	2.8	166.68	H-Bond (Protein Donor)	false
O2P	NZ	LYS- 79	3.54	0	Ionic (Protein Cationic)	false
C5'	CG	LYS- 79	3.79	0	Hydrophobic	false
C5'	CB	PRO- 86	3.88	0	Hydrophobic	false
O2P	N	MET- 87	2.82	160.14	H-Bond (Protein Donor)	false
C3H	CG	MET- 87	4.19	0	Hydrophobic	false
C4G	SD	MET- 87	3.63	0	Hydrophobic	false
O4'	NE1	TRP- 88	2.84	158.77	H-Bond (Protein Donor)	false
O1P	N	TRP- 88	2.97	134.85	H-Bond (Protein Donor)	false
O5H	ND2	ASN- 91	2.77	150.18	H-Bond (Protein Donor)	false
O4	OH	TYR- 133	2.87	154.81	H-Bond (Protein Donor)	false
O4	O	HOH- 314	2.83	179.96	H-Bond (Protein Donor)	false