scPDB - 4tm1 entry

Protein Data Bank Entry:

PDB ID : 4tm1

Resolution :2.390 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	100 %

Ligand binding site composition:

B-Factor:	24.440
Number of residues:	56
Including
Standard Amino Acids:	49
Non Standard Amino Acids:	1
Water Molecules:	6
Cofactors:	NAP
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.927	1569.375

% Hydrophobic	% Polar
42.15	57.85
According to VolSite

Ligand :

HET Code:	FDA
Formula:	C27H33N9O15P2
Molecular weight:	785.550 g/mol
DrugBank ID:	-
Buried Surface Area:	72.1 %
Polar Surface area:	381.04 Å2

Number of
H-Bond Acceptors:	21
H-Bond Donors:	9
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
47.4549	-1.29426	-59.2253

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
C4'	CG	PRO- 21	4.3	0	Hydrophobic	false
O1P	N	ALA- 22	2.92	158.3	H-Bond (Protein Donor)	false
O3B	OE2	GLU- 43	3.19	126.78	H-Bond (Ligand Donor)	false
O3B	OE1	GLU- 43	2.85	174.75	H-Bond (Ligand Donor)	false
O2B	OE2	GLU- 43	2.63	153.86	H-Bond (Ligand Donor)	false
O2B	NE	ARG- 44	3.32	135.06	H-Bond (Protein Donor)	false
N3A	N	ARG- 44	3.18	142.32	H-Bond (Protein Donor)	false
C1B	CG	ARG- 44	4.43	0	Hydrophobic	false
O3'	NE1	TRP- 50	3.21	156.1	H-Bond (Protein Donor)	false
O4'	NE1	TRP- 50	3.42	129.29	H-Bond (Protein Donor)	false
O4'	NE2	HIS- 51	2.75	152.62	H-Bond (Protein Donor)	false
C7M	CB	HIS- 51	3.91	0	Hydrophobic	false
C7M	CB	MET- 54	3.75	0	Hydrophobic	false
O4	N	GLN- 62	2.78	176.19	H-Bond (Protein Donor)	false
C6	CD	ARG- 104	4.03	0	Hydrophobic	false
N6A	O	VAL- 128	2.99	165.96	H-Bond (Ligand Donor)	false
N1A	N	VAL- 128	3.08	165.82	H-Bond (Protein Donor)	false
C1'	CD1	LEU- 166	4.45	0	Hydrophobic	false
C8M	CZ	TYR- 346	3.57	0	Hydrophobic	false
O2'	O	SER- 403	2.69	177.86	H-Bond (Ligand Donor)	false
C1'	CD2	LEU- 404	4.44	0	Hydrophobic	false
O2	N	LEU- 405	2.65	173.35	H-Bond (Protein Donor)	false
C3'	CD2	LEU- 405	3.82	0	Hydrophobic	false
C7M	C5N	NAP- 502	3.55	0	Hydrophobic	false
C9	C4D	NAP- 502	4.28	0	Hydrophobic	false
O2P	O	HOH- 606	2.84	166.73	H-Bond (Protein Donor)	false
O1P	O	HOH- 621	2.88	179.97	H-Bond (Protein Donor)	false
O3B	O	HOH- 652	3.11	179.98	H-Bond (Protein Donor)	false