scPDB - 4tm0 entry

Protein Data Bank Entry:

PDB ID : 4tm0

Resolution :2.740 Å

Experimental Method : X-ray

Deposition Date : 2014-05-30

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	KtzI
ID:	A8CF85_9PSEU
AC:	A8CF85
Organism:	Kutzneria sp. 744
Reign:	Bacteria
TaxID:	345341
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
B	4 %
C	96 %

Ligand binding site composition:

B-Factor:	22.271
Number of residues:	52
Including
Standard Amino Acids:	46
Non Standard Amino Acids:	2
Water Molecules:	4
Cofactors:	FAD
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.001	664.875

% Hydrophobic	% Polar
46.70	53.30
According to VolSite

Ligand :

HET Code:	NAP
Formula:	C21H25N7O17P3
Molecular weight:	740.381 g/mol
DrugBank ID:	DB03461
Buried Surface Area:	64.09 %
Polar Surface area:	405.54 Å2

Number of
H-Bond Acceptors:	21
H-Bond Donors:	5
Rings:	5
Aromatic rings:	3
Anionic atoms:	4
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
-25.8388	21.6077	36.3303

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
C5N	CE	MET- 54	4.38	0	Hydrophobic	false
N7N	O	LYS- 60	3.04	126.02	H-Bond (Ligand Donor)	false
C3N	CG	GLN- 62	4.16	0	Hydrophobic	false
O3B	N	GLY- 206	2.92	142.32	H-Bond (Protein Donor)	false
C2D	CB	GLN- 208	4.01	0	Hydrophobic	false
C4N	CG	GLN- 208	3.74	0	Hydrophobic	false
O1N	OG	SER- 209	2.85	158.1	H-Bond (Protein Donor)	false
O2N	N	SER- 209	3.06	158.59	H-Bond (Protein Donor)	false
C5N	CB	SER- 209	4.22	0	Hydrophobic	false
N7N	OE2	GLU- 212	3.27	137.91	H-Bond (Ligand Donor)	false
C1B	CG	PRO- 231	4.48	0	Hydrophobic	false
O1X	OH	TYR- 270	2.75	159.52	H-Bond (Protein Donor)	false
O3D	O	ASN- 275	2.89	140.21	H-Bond (Ligand Donor)	false
O2A	N	SER- 277	2.71	164.37	H-Bond (Protein Donor)	false
O3X	OG	SER- 277	2.87	165.34	H-Bond (Protein Donor)	false
C3B	CB	SER- 277	3.87	0	Hydrophobic	false
N6A	O	VAL- 310	2.93	176.84	H-Bond (Ligand Donor)	false
N1A	N	VAL- 310	2.9	160.28	H-Bond (Protein Donor)	false
C4D	C6	FAD- 501	4.4	0	Hydrophobic	false
C3N	C8M	FAD- 501	3.85	0	Hydrophobic	false
C5N	C7M	FAD- 501	3.28	0	Hydrophobic	false
O1N	O	HOH- 619	2.8	157.1	H-Bond (Protein Donor)	false