NPASS Compound

Structure

Physi-Chem Properties

Molecular Weight:	278.22
Volume:	326.919
LogP:	3.054
LogD:	3.448
LogS:	-4.272
# Rotatable Bonds:	10
TPSA:	37.3
# H-Bond Aceptor:	2
# H-Bond Donor:	1
# Rings:	0
# Heavy Atoms:	2

MedChem Properties

QED Drug-Likeness Score:	0.586
Synthetic Accessibility Score:	3.41
Fsp3:	0.611
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.648
MDCK Permeability:	2.81957327388227e-05
Pgp-inhibitor:	0.93
Pgp-substrate:	0.497
Human Intestinal Absorption (HIA):	0.177
20% Bioavailability (F20%):	0.601
30% Bioavailability (F30%):	0.01

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.811
Plasma Protein Binding (PPB):	85.73843383789062%
Volume Distribution (VD):	0.736
Pgp-substrate:	5.970192909240723%

ADMET: Metabolism

CYP1A2-inhibitor:	0.124
CYP1A2-substrate:	0.551
CYP2C19-inhibitor:	0.119
CYP2C19-substrate:	0.301
CYP2C9-inhibitor:	0.05
CYP2C9-substrate:	0.95
CYP2D6-inhibitor:	0.081
CYP2D6-substrate:	0.858
CYP3A4-inhibitor:	0.033
CYP3A4-substrate:	0.173

ADMET: Excretion

Clearance (CL):	4.78
Half-life (T1/2):	0.673

ADMET: Toxicity

hERG Blockers:	0.013
Human Hepatotoxicity (H-HT):	0.655
Drug-inuced Liver Injury (DILI):	0.017
AMES Toxicity:	0.001
Rat Oral Acute Toxicity:	0.002
Maximum Recommended Daily Dose:	0.956
Skin Sensitization:	0.923
Carcinogencity:	0.026
Eye Corrosion:	0.771
Eye Irritation:	0.915
Respiratory Toxicity:	0.034

Download Data

Data Type	Select
General Info & Identifiers & Properties
Structure MOL file
Source Organisms
Biological Activities
Similar NPs/Drugs

Natural Product: NPC217188

Natural Product ID:	NPC217188
*Common Name:**	(5E,9E)-13-Hydroxy-6,10,14-Trimethylpentadeca-5,9,14-Trien-2-One
IUPAC Name:	(5E,9E,13R)-13-hydroxy-6,10,14-trimethylpentadeca-5,9,14-trien-2-one
Synonyms:
Standard InCHIKey:	KUTNIFBDXANLKK-CUAZYIIYSA-N
Standard InCHI:	InChI=1S/C18H30O2/c1-14(2)18(20)13-12-16(4)9-6-8-15(3)10-7-11-17(5)19/h9-10,18,20H,1,6-8,11-13H2,2-5H3/b15-10+,16-9+/t18-/m1/s1
SMILES:	C/C(=CCC/C(=C/CCC(=O)C)/C)/CC[C@H](C(=C)C)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL502007
PubChem CID:	23426356
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001550] Sesquiterpenoids

*Note: the InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
**Note: the Chemical Classification was calculated by NPClassifier Version 1.5. Reference: PMID:34662515.

Species Source

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO15949	Cystophora moniliformis	Species	Sargassaceae	Eukaryota	n.a.	southern Australian	n.a.	PMID[18687007]
NPO15949	Cystophora moniliformis	Species	Sargassaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]

☑ Note for Reference:
In addition to directly collecting NP source organism data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated them from below databases:
☉ UNPD: Universal Natural Products Database [PMID: 23638153].
☉ StreptomeDB: a database of streptomycetes natural products [PMID: 33051671].
☉ TM-MC: a database of medicinal materials and chemical compounds in Northeast Asian traditional medicine [PMID: 26156871].
☉ TCM@Taiwan: a Traditional Chinese Medicine database [PMID: 21253603].
☉ TCMID: a Traditional Chinese Medicine database [PMID: 29106634].
☉ TCMSP: The traditional Chinese medicine systems pharmacology database and analysis platform [PMID: 24735618].
☉ HerDing: a herb recommendation system to treat diseases using genes and chemicals [PMID: 26980517].
☉ MetaboLights: a metabolomics database [PMID: 27010336].
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

NP Quantity Composition/Concentration

Organism ID	NP ID	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference

☑ Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP quantitative records for specific NP domains (e.g., NPS from foods or herbs) from domain-specific databases. These databases include:
☉ DUKE: Dr. Duke's Phytochemical and Ethnobotanical Databases.
☉ PHENOL EXPLORER: is the first comprehensive database on polyphenol content in foods [PMID: 24103452], its homepage can be accessed at here.
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

Biological Activity

Activity Type	# Activity
IC50	1
Others	1

Activity Type	# Activity
Cell Line	1
Organism	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT168	Cell Line	P388	Mus musculus	IC50	>	40000.0	nM	PMID[506873]
NPT330	Organism	Trichophyton mentagrophytes	Trichophyton mentagrophytes	IZ	=	1.0	mm	PMID[506873]

☑ Note for Activity Records:
☉ The quantitative biological activities were primarily integrated from ChEMBL (Version-30) database and were also directly collected from PubMed literature. PubMed PMID was provided as the reference link for each activity record.

Chemically structural similarity: I. Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes 4,3285 NPs with experimentally-derived bioactivity available in NPASS)

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules. Tc lies between [0, 1] where '1' indicates the highest similarity. What is Tanimoto coefficient

● The left chart: Distribution of similarity level between NPC217188 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	118
0.1-0.2	2806
0.2-0.3	15670
0.3-0.4	13539
0.4-0.5	6767
0.5-0.6	2915
0.6-0.7	768
0.7-0.8	101
0.8-0.85	6
0.85-0.9	6
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
0.88	High Similarity	NPC267110
0.8627	High Similarity	NPC288381
0.8627	High Similarity	NPC20934
0.8627	High Similarity	NPC225974
0.8462	Intermediate Similarity	NPC474495
0.8462	Intermediate Similarity	NPC473672
0.8333	Intermediate Similarity	NPC189677
0.8246	Intermediate Similarity	NPC278202
0.8214	Intermediate Similarity	NPC268185
0.8148	Intermediate Similarity	NPC474496
0.7966	Intermediate Similarity	NPC64971
0.7843	Intermediate Similarity	NPC140501
0.7818	Intermediate Similarity	NPC61177
0.7818	Intermediate Similarity	NPC284224
0.7797	Intermediate Similarity	NPC327112
0.7656	Intermediate Similarity	NPC236208
0.7619	Intermediate Similarity	NPC106613
0.7586	Intermediate Similarity	NPC71755
0.7586	Intermediate Similarity	NPC193975
0.7544	Intermediate Similarity	NPC317899
0.7544	Intermediate Similarity	NPC227135
0.746	Intermediate Similarity	NPC137163
0.7458	Intermediate Similarity	NPC226848
0.7455	Intermediate Similarity	NPC151782
0.7455	Intermediate Similarity	NPC71053
0.7455	Intermediate Similarity	NPC59408
0.7451	Intermediate Similarity	NPC116934
0.7419	Intermediate Similarity	NPC475221
0.7419	Intermediate Similarity	NPC470320
0.7407	Intermediate Similarity	NPC153538
0.7377	Intermediate Similarity	NPC113293
0.7377	Intermediate Similarity	NPC260573
0.7368	Intermediate Similarity	NPC137538
0.7368	Intermediate Similarity	NPC49059
0.7368	Intermediate Similarity	NPC110732
0.7368	Intermediate Similarity	NPC256209
0.7344	Intermediate Similarity	NPC96962
0.7344	Intermediate Similarity	NPC269985
0.7333	Intermediate Similarity	NPC122239
0.7333	Intermediate Similarity	NPC475931
0.7333	Intermediate Similarity	NPC318306
0.7333	Intermediate Similarity	NPC322002
0.7321	Intermediate Similarity	NPC473705
0.7321	Intermediate Similarity	NPC35756
0.7302	Intermediate Similarity	NPC136164
0.7302	Intermediate Similarity	NPC255863
0.7302	Intermediate Similarity	NPC245947
0.7288	Intermediate Similarity	NPC323436
0.7273	Intermediate Similarity	NPC72699
0.7273	Intermediate Similarity	NPC473487
0.7273	Intermediate Similarity	NPC474460
0.7255	Intermediate Similarity	NPC249801
0.7255	Intermediate Similarity	NPC46248
0.7241	Intermediate Similarity	NPC281590
0.7241	Intermediate Similarity	NPC232247
0.7241	Intermediate Similarity	NPC251666
0.7241	Intermediate Similarity	NPC52264
0.7241	Intermediate Similarity	NPC329686
0.7213	Intermediate Similarity	NPC243532
0.7213	Intermediate Similarity	NPC328311
0.7206	Intermediate Similarity	NPC227396
0.7188	Intermediate Similarity	NPC472072
0.717	Intermediate Similarity	NPC160628
0.7167	Intermediate Similarity	NPC155025
0.7167	Intermediate Similarity	NPC181872
0.7164	Intermediate Similarity	NPC67076
0.7164	Intermediate Similarity	NPC474884
0.7164	Intermediate Similarity	NPC319163
0.7143	Intermediate Similarity	NPC226592
0.7143	Intermediate Similarity	NPC180840
0.7143	Intermediate Similarity	NPC93639
0.7121	Intermediate Similarity	NPC143396
0.7119	Intermediate Similarity	NPC48891
0.7119	Intermediate Similarity	NPC472808
0.7119	Intermediate Similarity	NPC327388
0.7119	Intermediate Similarity	NPC40148
0.7119	Intermediate Similarity	NPC324224
0.7101	Intermediate Similarity	NPC474011
0.7097	Intermediate Similarity	NPC477829
0.7097	Intermediate Similarity	NPC201939
0.7097	Intermediate Similarity	NPC321838
0.7097	Intermediate Similarity	NPC269737
0.7091	Intermediate Similarity	NPC85079
0.7091	Intermediate Similarity	NPC31194
0.7091	Intermediate Similarity	NPC302310
0.7091	Intermediate Similarity	NPC248884
0.7077	Intermediate Similarity	NPC26500
0.7077	Intermediate Similarity	NPC99619
0.7069	Intermediate Similarity	NPC300121
0.7069	Intermediate Similarity	NPC48058
0.7069	Intermediate Similarity	NPC473532
0.7059	Intermediate Similarity	NPC323437
0.7059	Intermediate Similarity	NPC275098
0.7059	Intermediate Similarity	NPC201562
0.7059	Intermediate Similarity	NPC269823
0.7059	Intermediate Similarity	NPC186042
0.7059	Intermediate Similarity	NPC29542
0.7049	Intermediate Similarity	NPC329249
0.7049	Intermediate Similarity	NPC322186
0.7049	Intermediate Similarity	NPC473652
0.7037	Intermediate Similarity	NPC124183
0.7037	Intermediate Similarity	NPC55063
0.7037	Intermediate Similarity	NPC8610
0.7037	Intermediate Similarity	NPC35141
0.7037	Intermediate Similarity	NPC262558
0.7037	Intermediate Similarity	NPC19834
0.7031	Intermediate Similarity	NPC474304
0.7031	Intermediate Similarity	NPC474329
0.7031	Intermediate Similarity	NPC317881
0.7031	Intermediate Similarity	NPC323045
0.7015	Intermediate Similarity	NPC318766
0.7015	Intermediate Similarity	NPC286154
0.7	Intermediate Similarity	NPC52012
0.7	Intermediate Similarity	NPC211752
0.7	Intermediate Similarity	NPC16279
0.7	Intermediate Similarity	NPC182840
0.7	Intermediate Similarity	NPC255042
0.7	Intermediate Similarity	NPC281230
0.7	Intermediate Similarity	NPC44542
0.7	Intermediate Similarity	NPC283502
0.7	Intermediate Similarity	NPC29091
0.7	Intermediate Similarity	NPC192843
0.7	Intermediate Similarity	NPC103213
0.7	Intermediate Similarity	NPC323498
0.7	Intermediate Similarity	NPC323597
0.7	Intermediate Similarity	NPC256640
0.7	Intermediate Similarity	NPC205615
0.7	Intermediate Similarity	NPC469646
0.6984	Remote Similarity	NPC29697
0.6981	Remote Similarity	NPC101616
0.697	Remote Similarity	NPC117804
0.6964	Remote Similarity	NPC328784
0.6964	Remote Similarity	NPC291437
0.6964	Remote Similarity	NPC59051
0.6949	Remote Similarity	NPC473910
0.6949	Remote Similarity	NPC473896
0.6949	Remote Similarity	NPC473735
0.6949	Remote Similarity	NPC475353
0.6949	Remote Similarity	NPC477725
0.6949	Remote Similarity	NPC473725
0.6949	Remote Similarity	NPC471239
0.6949	Remote Similarity	NPC473721
0.6949	Remote Similarity	NPC477726
0.6939	Remote Similarity	NPC185839
0.6935	Remote Similarity	NPC81896
0.6935	Remote Similarity	NPC321919
0.6935	Remote Similarity	NPC99487
0.6923	Remote Similarity	NPC83965
0.6923	Remote Similarity	NPC256766
0.6923	Remote Similarity	NPC213538
0.6912	Remote Similarity	NPC95863
0.6909	Remote Similarity	NPC91495
0.6901	Remote Similarity	NPC471061
0.6866	Remote Similarity	NPC250928
0.6866	Remote Similarity	NPC10758
0.6866	Remote Similarity	NPC470436
0.6857	Remote Similarity	NPC474885
0.6852	Remote Similarity	NPC191337
0.6852	Remote Similarity	NPC76976
0.6852	Remote Similarity	NPC117572
0.6852	Remote Similarity	NPC24824
0.6852	Remote Similarity	NPC210560
0.6852	Remote Similarity	NPC165651
0.6842	Remote Similarity	NPC129263
0.6842	Remote Similarity	NPC48162
0.6833	Remote Similarity	NPC477201
0.6833	Remote Similarity	NPC470969
0.6833	Remote Similarity	NPC325977
0.6833	Remote Similarity	NPC470968
0.6833	Remote Similarity	NPC161838
0.6833	Remote Similarity	NPC473847
0.6833	Remote Similarity	NPC477661
0.6833	Remote Similarity	NPC471960
0.6833	Remote Similarity	NPC475384
0.6833	Remote Similarity	NPC470967
0.6833	Remote Similarity	NPC470966
0.6825	Remote Similarity	NPC325929
0.6825	Remote Similarity	NPC320305
0.6825	Remote Similarity	NPC321867
0.6825	Remote Similarity	NPC207007
0.6825	Remote Similarity	NPC64985
0.6825	Remote Similarity	NPC68679
0.6825	Remote Similarity	NPC271282
0.6825	Remote Similarity	NPC26810
0.6825	Remote Similarity	NPC55376
0.6825	Remote Similarity	NPC168407
0.6825	Remote Similarity	NPC328776
0.6825	Remote Similarity	NPC475984
0.6825	Remote Similarity	NPC66460
0.6818	Remote Similarity	NPC49863
0.6818	Remote Similarity	NPC25298
0.6818	Remote Similarity	NPC278895
0.6818	Remote Similarity	NPC478097
0.6806	Remote Similarity	NPC478122
0.6806	Remote Similarity	NPC475994
0.68	Remote Similarity	NPC40434
0.68	Remote Similarity	NPC34873
0.6792	Remote Similarity	NPC252978
0.6792	Remote Similarity	NPC301972
0.6786	Remote Similarity	NPC471280

Chemically structural similarity: II. Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

● The left chart: Distribution of similarity level between NPC217188 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	113
0.1-0.2	3111
0.2-0.3	4176
0.3-0.4	1309
0.4-0.5	314
0.5-0.6	90
0.6-0.7	35
0.7-0.8	2
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.7843	Intermediate Similarity	NPD4265	Approved
0.7797	Intermediate Similarity	NPD4246	Clinical (unspecified phase)
0.7	Intermediate Similarity	NPD5783	Phase 3
0.6875	Remote Similarity	NPD3197	Phase 1
0.6852	Remote Similarity	NPD39	Approved
0.6852	Remote Similarity	NPD4222	Approved
0.6825	Remote Similarity	NPD368	Approved
0.6818	Remote Similarity	NPD4247	Clinical (unspecified phase)
0.6786	Remote Similarity	NPD3173	Approved
0.6667	Remote Similarity	NPD342	Phase 1
0.6667	Remote Similarity	NPD4627	Clinical (unspecified phase)
0.6613	Remote Similarity	NPD6109	Phase 1
0.661	Remote Similarity	NPD3172	Approved
0.6575	Remote Similarity	NPD5784	Clinical (unspecified phase)
0.6552	Remote Similarity	NPD6927	Phase 3
0.65	Remote Similarity	NPD3196	Approved
0.65	Remote Similarity	NPD3195	Phase 2
0.65	Remote Similarity	NPD3194	Approved
0.65	Remote Similarity	NPD4266	Approved
0.6481	Remote Similarity	NPD5326	Phase 3
0.6462	Remote Similarity	NPD2664	Clinical (unspecified phase)
0.6418	Remote Similarity	NPD7331	Phase 2
0.6418	Remote Similarity	NPD3704	Approved
0.64	Remote Similarity	NPD4252	Approved
0.6351	Remote Similarity	NPD4268	Approved
0.6351	Remote Similarity	NPD4271	Approved
0.6316	Remote Similarity	NPD5343	Approved
0.625	Remote Similarity	NPD3174	Discontinued
0.6234	Remote Similarity	NPD4270	Approved
0.6234	Remote Similarity	NPD4269	Approved
0.6216	Remote Similarity	NPD4756	Discovery
0.6212	Remote Similarity	NPD3210	Clinical (unspecified phase)
0.6207	Remote Similarity	NPD4220	Pre-registration
0.619	Remote Similarity	NPD8779	Phase 3
0.6184	Remote Similarity	NPD4822	Approved
0.6184	Remote Similarity	NPD4819	Approved
0.6184	Remote Similarity	NPD5790	Clinical (unspecified phase)
0.6184	Remote Similarity	NPD8259	Clinical (unspecified phase)
0.6184	Remote Similarity	NPD4821	Approved
0.6184	Remote Similarity	NPD4820	Approved
0.6154	Remote Similarity	NPD5362	Discontinued
0.6154	Remote Similarity	NPD5332	Approved
0.6154	Remote Similarity	NPD6110	Phase 1
0.6154	Remote Similarity	NPD5331	Approved
0.6154	Remote Similarity	NPD7154	Phase 3
0.6111	Remote Similarity	NPD4732	Discontinued
0.6104	Remote Similarity	NPD4790	Discontinued
0.6071	Remote Similarity	NPD6096	Approved
0.6071	Remote Similarity	NPD6097	Approved
0.6032	Remote Similarity	NPD4219	Approved
0.6029	Remote Similarity	NPD2685	Clinical (unspecified phase)
0.6026	Remote Similarity	NPD3667	Approved
0.6	Remote Similarity	NPD28	Approved
0.6	Remote Similarity	NPD5363	Approved
0.6	Remote Similarity	NPD29	Approved
0.5974	Remote Similarity	NPD5368	Approved
0.5946	Remote Similarity	NPD8264	Approved
0.5942	Remote Similarity	NPD6108	Clinical (unspecified phase)
0.5926	Remote Similarity	NPD5786	Approved
0.5897	Remote Similarity	NPD5369	Approved
0.5893	Remote Similarity	NPD9411	Phase 1
0.5875	Remote Similarity	NPD3133	Approved
0.5875	Remote Similarity	NPD4786	Approved
0.5875	Remote Similarity	NPD3665	Phase 1
0.5875	Remote Similarity	NPD3666	Approved
0.5846	Remote Similarity	NPD585	Clinical (unspecified phase)
0.5823	Remote Similarity	NPD6435	Approved
0.5802	Remote Similarity	NPD6082	Clinical (unspecified phase)
0.5797	Remote Similarity	NPD7341	Phase 2
0.5789	Remote Similarity	NPD5776	Phase 2
0.5789	Remote Similarity	NPD6925	Approved
0.5763	Remote Similarity	NPD622	Approved
0.5732	Remote Similarity	NPD3618	Phase 1
0.5732	Remote Similarity	NPD5279	Phase 3
0.5732	Remote Similarity	NPD4249	Approved
0.5714	Remote Similarity	NPD7322	Clinical (unspecified phase)
0.5714	Remote Similarity	NPD7145	Approved
0.5714	Remote Similarity	NPD5370	Suspended
0.5694	Remote Similarity	NPD6923	Approved
0.5694	Remote Similarity	NPD6922	Approved
0.5679	Remote Similarity	NPD6400	Clinical (unspecified phase)
0.5663	Remote Similarity	NPD4250	Approved
0.5663	Remote Similarity	NPD4251	Approved
0.5658	Remote Similarity	NPD818	Approved
0.5658	Remote Similarity	NPD819	Approved
0.5647	Remote Similarity	NPD5785	Approved
0.5641	Remote Similarity	NPD6929	Approved
0.5616	Remote Similarity	NPD7144	Approved
0.5616	Remote Similarity	NPD7143	Approved
0.5616	Remote Similarity	NPD3212	Clinical (unspecified phase)
0.561	Remote Similarity	NPD1696	Phase 3
0.56	Remote Similarity	NPD6926	Approved
0.56	Remote Similarity	NPD6924	Approved

Bioactivity similarity: Similar Natural Products in NPASS

Bioactivity similarity was calculated based on bioactivity descriptors of compounds. The bioactivity descriptors were calculated by a recently developed AI algorithm Chemical Checker (CC) [Nature Biotechnology, 38:1087–1096, 2020; Nature Communications, 12:3932, 2021], which evaluated bioactivity similarities at five levels:
☉ A: chemistry similarity;
☉ B: biological targets similarity;
☉ C: networks similarity;
☉ D: cell-based bioactivity similarity;
☉ E: similarity based on clinical data.

Those 5 categories of CC bioactivity descriptors were calculated and then subjected to manifold projection using UMAP algorithm, to project all NPs on a 2-Dimensional space. The current NP was highlighted with a small circle in the 2-D map. Below figures: left-to-right, A-to-E.

A: chemistry similarity

B: biological targets similarity

C: networks similarity

D: cell-based bioactivity similarity

E: similarity based on clinical data