Basic information

CPKB ID	CP00004
IUPAC Name	3-benzyl-6,6-dimethyl-9-[6-(oxiran-2-yl)-6-oxohexyl]-1,4,7,10-tetrazabicyclo[10.3.0]pentadecane-2,5,8,11-tetrone
Synonyms	53342-16-8 Bs-1305 Chlamydocin

Legend

Structure

Molecular Formula	C28H38N4O6
Molecular Weight	526.2791349 g/mol
SMILES RUN SEA Predictions	CC1(C)NC(=O)[C@H](CCCCCC(=O)[C@@H]2CO2)NC(=O)[C@@H]2CCCN2C(=O)[C@H](Cc2ccccc2)NC1=O PubChem\|2706
InChI	InChI=1S/C28H38N4O6/c1-28(2)27(37)30-20(16-18-10-5-3-6-11-18)26(36)32-15-9-13-21(32)25(35)29-19(24(34)31-28)12-7-4-8-14-22(33)23-17-38-23/h3,5-6,10-11,19-21,23H,4,7-9,12-17H2,1-2H3,(H,29,35)(H,30,37)(H,31,34)
InChIKey	SGYJGGKDGBXCNY-RFWGSTRHNA-N

2D Structure PubChem\|2706
3D Structure PubChem\|2706

Sequence

IUPAC Condensed	cyclo[Aib-DL-Phe-DL-Pro-DL-Asu(Unk)] PubChem\|2706
Amino acid chain	Aib(1)--DL-Phe--DL-Pro--DL-Asu(Unk)(1) CyclicPepedia\|PP
Graph representation	Aib,DL-Phe,DL-Pro,DL-Asu(Unk) @0,3 CyclicPepedia\|PP
One letter code from Structure	AFPA CyclicPepedia\|Struct2seq
Amino acid chain from Structure	Aib(1)--Phe--Pro--C10:0-OH(9)-NH2(2)-oxo(8)(1) CyclicPepedia\|Struct2seq
Description of the conversion sequence	The one letter code and Amino acid chain derived from the structural transformation may be inconsistent, with the Amino acid chain containing Essential Amino acid and the one letter code not.
svg Image PubChem\|2706

Chemical and Physical Properties

CyclicPepedia|Struc2Seq + PP

Structure Properties

Property Name	Property Value
Exact Mass	526.2791349
Number of Rings	4.0
Complexity	1.0
XlogP3 AA	1.0165
Heavy Atom Count	38.0
Hydrogen Bond Donor Count	3.0
Hydrogen Bond Acceptor Count	6.0
Rotatable Bond Count	9.0

Property Name	Property Value
Formal Charge	0.0
Refractivity	138.7961
Rule_of_Five	0.0
Number of Atoms	38.0
Topological Polar Surface Area	137.21
Refractivity	138.7961
Veber Rule	1.0
Ghose Filter	0.0

Property Name	Property Value
RDKit Fingerprint	01000010100000100100100011011000010000100111010000100010100000000010101111101100100110000110110011010101000001101010011001110010000001001000110000001111000110010100001010000110000110011111100100100010101001101000100001000000010101000101001110001100011100101111000110001000000010001001000000000110011010010010101101000101010100000110111011011110101001000011111000000001000010000000000000000011010100000100000100001100000010000010101000110011110011100010000100011010111000010000000000000010001110010101100000101100110000100100101110010101100110000100100010010110001000111100010010000000000010111000101000110001001010011000111000101001101000100100000010100110000001000110001010000000010101011100011100010100100101000000000100100011001001011000100010010010001110101010011111010110000001101011001010001000001100001100100100101001111010110010010011101001000000110010011101100101010100000100111000000011101101100011111001010101011110011010000000011110001000001100010001010000011000011100001000000011010100000100000000101111001111110011110110001010100000001010000000001000111101100001000001001101110110100001001101010010000000101100000111001001010000000000101000101000100110100110100111001001011010001110000001000100000011001101010010100000011100010111001010010000100101000010101000100000000010110000110001101001111010100000000001100010100001000011101110000011010111110001010000011000000101001000001000000001000001001100000001100101100010001100000011111110001001001011000100000110011000100001010000111011011000000000100100110111000001110000001000010000010010100100000010100000000110100111001101000101100010000001010010000001000000110110110001000100000000000001010000000001000011000100001010010001000000001001011110000100110101000001010110001000100000100011011000010100000010010110100000000000100001010010000000000011111001101101000010111000011110101111110010000000100000000000111011100001010000001101101100001100101101000101010000010101110010000111110110000001011111011011001010000001001001100110000101000100100010000000000001101111000100000000111000000011
Morgan Fingerprint	0000110000100000000100000000100001001000001000000000000000000000100000000000000010000000001000000000000000000000000100010000000000000000000000000000000000000000000000000000000100000000000000000000000000000000000000000000000000000001000000000001000000100000000000000000000000000000000000001000000000000100000000000010000000000000000000100000100000000000000110000000000000000000000000000000010000000000000000000000000000000000000000001000000000000010000000001011000000000000000000000000000000000010000000000001000000000000001000000000000000001000000000000000000000100000000000000000000000000000000000000000000000000001000000000000000000100000100000000010000010000000010000000000000000011000000000000000000000000000010000000000001000100000000000000000000000000000000000000000000000000000000000000000000000100001000100000000000000000000100000000000000001000000001010000000000000000000000010010000010000010000100000000000000000000010000000010000000000000000000001000000000000000000000000000000000000000000010000100000000000010000
MACCS Keys	00000000000000001000001000000000000000000000000000000010010000000010000010100001000101000111100110001100110001111000011011100001110110001110101100111111111111111111110

Sequence Properties

Property Name	Property Value
Boman Index	-1.65
Instability	103.8
Charge	-0.00201570060725275
Aliphatic Index	50.0

Binding Target

Other evidence

Property Name	Property ID
TTD	D0UC6H
DrugMAP	DM89DQP

Manufacturers

Manufacturers Name	Value
CreativePeptides	3-Benzyl-6,6-Dimethyl-9-[6-(Oxiran-2-Yl)-6-Oxohexyl]-1,4,7,10-Tetrazabicyclo[10.3.0]Pentadecane-2,5,8,11-Tetrone
Bayer healthcare pharmaceuticals	3-Benzyl-6,6-Dimethyl-9-[6-(Oxiran-2-Yl)-6-Oxohexyl]-1,4,7,10-Tetrazabicyclo[10.3.0]Pentadecane-2,5,8,11-Tetrone
Upsher smith laboratories	3-Benzyl-6,6-Dimethyl-9-[6-(Oxiran-2-Yl)-6-Oxohexyl]-1,4,7,10-Tetrazabicyclo[10.3.0]Pentadecane-2,5,8,11-Tetrone
Merck	3-Benzyl-6,6-Dimethyl-9-[6-(Oxiran-2-Yl)-6-Oxohexyl]-1,4,7,10-Tetrazabicyclo[10.3.0]Pentadecane-2,5,8,11-Tetrone

Manufacturers Name	Value
Apotex	3-Benzyl-6,6-Dimethyl-9-[6-(Oxiran-2-Yl)-6-Oxohexyl]-1,4,7,10-Tetrazabicyclo[10.3.0]Pentadecane-2,5,8,11-Tetrone
Baxter Healthcare Corp	3-Benzyl-6,6-Dimethyl-9-[6-(Oxiran-2-Yl)-6-Oxohexyl]-1,4,7,10-Tetrazabicyclo[10.3.0]Pentadecane-2,5,8,11-Tetrone
Pharmasources	3-Benzyl-6,6-Dimethyl-9-[6-(Oxiran-2-Yl)-6-Oxohexyl]-1,4,7,10-Tetrazabicyclo[10.3.0]Pentadecane-2,5,8,11-Tetrone
Novartis	3-Benzyl-6,6-Dimethyl-9-[6-(Oxiran-2-Yl)-6-Oxohexyl]-1,4,7,10-Tetrazabicyclo[10.3.0]Pentadecane-2,5,8,11-Tetrone
AstraZeneca	3-Benzyl-6,6-Dimethyl-9-[6-(Oxiran-2-Yl)-6-Oxohexyl]-1,4,7,10-Tetrazabicyclo[10.3.0]Pentadecane-2,5,8,11-Tetrone

Forecasting tools

Forecasting tools	Value
Structure to Sequence	CC1(C)NC(=O)[C@H](CCCCCC(=O)[C@@H]2CO2)NC(=O)[C@@H]2CCCN2C(=O)[C@H](Cc2ccccc2)NC1=O
Structure Properties	CC1(C)NC(=O)[C@H](CCCCCC(=O)[C@@H]2CO2)NC(=O)[C@@H]2CCCN2C(=O)[C@H](Cc2ccccc2)NC1=O
Sequence to Structure	AFPA
Sequence Properties	AFPA
Expasy ProtParam Tool	AFPA
SEA	RUN SEA Predictions

Information Source

Property Name	Property ID
Patents	SGYJGGKDGBXCNY-RFWGSTRHNA-N
pubchem	2706
Drugbank	3-Benzyl-6,6-Dimethyl-9-[6-(Oxiran-2-Yl)-6-Oxohexyl]-1,4,7,10-Tetrazabicyclo[10.3.0]Pentadecane-2,5,8,11-Tetrone
DRAMP3	3-Benzyl-6,6-Dimethyl-9-[6-(Oxiran-2-Yl)-6-Oxohexyl]-1,4,7,10-Tetrazabicyclo[10.3.0]Pentadecane-2,5,8,11-Tetrone
Uniprot	3-Benzyl-6,6-Dimethyl-9-[6-(Oxiran-2-Yl)-6-Oxohexyl]-1,4,7,10-Tetrazabicyclo[10.3.0]Pentadecane-2,5,8,11-Tetrone
Cybase	3-Benzyl-6,6-Dimethyl-9-[6-(Oxiran-2-Yl)-6-Oxohexyl]-1,4,7,10-Tetrazabicyclo[10.3.0]Pentadecane-2,5,8,11-Tetrone
CONOSERVER	3-Benzyl-6,6-Dimethyl-9-[6-(Oxiran-2-Yl)-6-Oxohexyl]-1,4,7,10-Tetrazabicyclo[10.3.0]Pentadecane-2,5,8,11-Tetrone
BindingDB	CC1(C)NC(=O)[C@H](CCCCCC(=O)[C@@H]2CO2)NC(=O)[C@@H]2CCCN2C(=O)[C@H](Cc2ccccc2)NC1=O
CHEMBL	3-Benzyl-6,6-Dimethyl-9-[6-(Oxiran-2-Yl)-6-Oxohexyl]-1,4,7,10-Tetrazabicyclo[10.3.0]Pentadecane-2,5,8,11-Tetrone
CTD	3-Benzyl-6,6-Dimethyl-9-[6-(Oxiran-2-Yl)-6-Oxohexyl]-1,4,7,10-Tetrazabicyclo[10.3.0]Pentadecane-2,5,8,11-Tetrone
Wikipedia	3-Benzyl-6,6-Dimethyl-9-[6-(Oxiran-2-Yl)-6-Oxohexyl]-1,4,7,10-Tetrazabicyclo[10.3.0]Pentadecane-2,5,8,11-Tetrone
KEGG Compound/Drug	3-Benzyl-6,6-Dimethyl-9-[6-(Oxiran-2-Yl)-6-Oxohexyl]-1,4,7,10-Tetrazabicyclo[10.3.0]Pentadecane-2,5,8,11-Tetrone
CHEBI	SGYJGGKDGBXCNY-RFWGSTRHNA-N
EPA DSSTox	3-Benzyl-6,6-Dimethyl-9-[6-(Oxiran-2-Yl)-6-Oxohexyl]-1,4,7,10-Tetrazabicyclo[10.3.0]Pentadecane-2,5,8,11-Tetrone
FDA Global Substance Registration System (GSRS)	3-Benzyl-6,6-Dimethyl-9-[6-(Oxiran-2-Yl)-6-Oxohexyl]-1,4,7,10-Tetrazabicyclo[10.3.0]Pentadecane-2,5,8,11-Tetrone
DTP/NCI	3-Benzyl-6,6-Dimethyl-9-[6-(Oxiran-2-Yl)-6-Oxohexyl]-1,4,7,10-Tetrazabicyclo[10.3.0]Pentadecane-2,5,8,11-Tetrone
Chemspider	SGYJGGKDGBXCNY-RFWGSTRHNA-N

Reference

Pubmed_ID	Title	DOI	Journal
3806605	Analogues of the cytostatic and antimitogenic agents chlamydocin and HC-toxin: synthesis and biological activity of chloromethyl ketone and diazomethyl ketone functionalized cyclic tetrapeptides	10.1021/jm00384a013.	J Med Chem
Analogues of the cytostatic and antimitogenic agents chlamydocin and HC-toxin: synthesis and biological activity of chloromethyl ketone and diazomethyl ketone functionalized cyclic tetrapeptides Abstract The synthesis and biological activity of four novel analogues of the cytostatic and antimitogenic agents chlamydocin and HC-toxin are reported in which the natural products' reactive epoxy ketone side-chain moiety is replaced by a chloromethyl or a diazomethyl ketone functionality, but the respective 12-membered cyclic tetrapeptide ring systems are retained. Syntheses of the linear tetrapeptide sequences were, in each case, achieved by conventional methodology and designed such that cyclization would be onto proline. The use of suitably protected L-2-aminosuberic acid (Asu) enabled the ready assimilation of the desired chloromethyl and diazomethyl ketone functionalities after cyclization. Cyclization was accomplished by using bis(2-oxo-3-oxazolidinyl)phosphinic chloride (BOP-Cl). Yields of cyclic product were comparable to or, in the case of the HC-toxin ring system, better than those previously reported. Liberation of the Asu-side-chain acid and manipulation to the required functionalities via mixed anhydride to the diazomethyl ketone and quenching with HCl to yield the chloromethyl ketone was achieved in excellent yield for the HC-toxin analogues but in only moderate yield for the chlamydocin analogue. The antimitogenic activities of HC-toxin chloromethyl ketone (IC50 = 30-40 ng/mL) and chlamydocin chloromethyl ketone (IC50 = 3-10 ng/mL) were found to be 3-4-fold lower than those of the natural products themselves. The diazomethyl ketone analogue of HC-toxin was found to be inactive (IC50 greater than 2000 ng/mL). A modification of the HC-toxin peptide ring system, L-Phe3-HC-toxin chloromethyl ketone was found not to be a more active analogue (IC50 = 40-100 ng/mL). The nature of the putative target molecule, the binding interactions of the various analogues and the contribution of rate of inhibition toward activity are briefly discussed. The chloromethyl ketones herein reported constitute the most potent synthetic antimitogenic cyclic tetrapeptide analogues yet designed."
3918884	Reciprocal biological activities of the cyclic tetrapeptides chlamydocin and HC-toxin	10.1007/BF02004498.	Experientia
Reciprocal biological activities of the cyclic tetrapeptides chlamydocin and HC-toxin Abstract Chlamydocin, a potent cytostatic agent against cultured mammalian cells, and HC-toxin, a host-specific phytotoxin, are cyclic tetrapeptides containing the same epoxide alpha-amino acid. We show here that these compounds have reciprocal biological activity; HC-toxin is cytostatic against cultured mastocytoma cells, and chlamydocin has host-specific toxin activity against maize. Chlamydocin and another related cyclic peptide, Cyl-2, are less host-specific than HC-toxin because maize tolerant to HC-toxin is more sensitive to chlamydocin and Cyl-2.
4857466	Isolation and structural clarification of chlamydocin	10.1002/hlca.19740570306.	Helv Chim Acta
Isolation and structural clarification of chlamydocin Abstract No profile to view
6826281	Conformational studies of cyclic tetrapeptides. Evidence for a bis gamma-turn conformation for chlamydocin and Ala4-chlamydocin in nonpolar solvents	None	Int J Pept Protein Res
Conformational studies of cyclic tetrapeptides. Evidence for a bis gamma-turn conformation for chlamydocin and Ala4-chlamydocin in nonpolar solvents Abstract The conformations of chlamydocin and cyclo (Ala-Aib-Phe-D-Pro) (Ala4-chlamydocin) in chloroform have been investigated by nuclear magnetic resonance, infrared and circular dichroism spectroscopy. The data obtained from these experiments establish an all transoid, bis gamma-turn conformation for both compounds in chloroform with the following torsional angles (+/- 20 degrees): Ala4-chlamydocin: Aib, phi + 60 degrees, psi - 50 degrees; omega + 160 degrees; Phe phi - 120 degrees, psi + 120 degrees, omega - 160 degrees; D-Pro phi + 60 degrees, psi - 55 degrees, omega + 160 degrees; Ala phi - 110 degrees, psi + 110 degrees, omega - 160 degrees. Chlamydocin adopts a closely related conformation in neat chloroform. Nuclear Overhauser Effect (NOE) data are utilized to assign amide bond geometries in the cyclic tetrapeptide ring system.