NPASS Compound

Structure

Physi-Chem Properties

Molecular Weight:	256.2
Volume:	289.094
LogP:	1.975
LogD:	2.059
LogS:	-2.207
# Rotatable Bonds:	8
TPSA:	60.69
# H-Bond Aceptor:	3
# H-Bond Donor:	3
# Rings:	0
# Heavy Atoms:	3

MedChem Properties

QED Drug-Likeness Score:	0.585
Synthetic Accessibility Score:	3.886
Fsp3:	0.733
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
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:	-4.343
MDCK Permeability:	2.2309006453724578e-05
Pgp-inhibitor:	0.022
Pgp-substrate:	0.027
Human Intestinal Absorption (HIA):	0.006
20% Bioavailability (F20%):	0.044
30% Bioavailability (F30%):	0.058

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.884
Plasma Protein Binding (PPB):	66.8021469116211%
Volume Distribution (VD):	1.229
Pgp-substrate:	31.303346633911133%

ADMET: Metabolism

CYP1A2-inhibitor:	0.014
CYP1A2-substrate:	0.116
CYP2C19-inhibitor:	0.022
CYP2C19-substrate:	0.752
CYP2C9-inhibitor:	0.014
CYP2C9-substrate:	0.453
CYP2D6-inhibitor:	0.008
CYP2D6-substrate:	0.062
CYP3A4-inhibitor:	0.257
CYP3A4-substrate:	0.237

ADMET: Excretion

Clearance (CL):	8.021
Half-life (T1/2):	0.608

ADMET: Toxicity

hERG Blockers:	0.015
Human Hepatotoxicity (H-HT):	0.051
Drug-inuced Liver Injury (DILI):	0.012
AMES Toxicity:	0.003
Rat Oral Acute Toxicity:	0.123
Maximum Recommended Daily Dose:	0.929
Skin Sensitization:	0.521
Carcinogencity:	0.125
Eye Corrosion:	0.129
Eye Irritation:	0.71
Respiratory Toxicity:	0.859

Download Data

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

Natural Product: NPC227135

Natural Product ID:	NPC227135
*Common Name:**	1,6-Farnesadiene-3,10,11-Triol
IUPAC Name:	(3S,6E,10S)-2,6,10-trimethyldodeca-6,11-diene-2,3,10-triol
Synonyms:
Standard InCHIKey:	BGUYVWYUIXKRDO-SIRQDLBWSA-N
Standard InCHI:	InChI=1S/C15H28O3/c1-6-15(5,18)11-7-8-12(2)9-10-13(16)14(3,4)17/h6,8,13,16-18H,1,7,9-11H2,2-5H3/b12-8+/t13-,15+/m0/s1
SMILES:	C=C[C@](C)(CC/C=C(C)/CC[C@@H](C(C)(C)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL487791
PubChem CID:	10355067
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
NPO10467	Resupinatus leightonii	Species	Tricholomataceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11000039]
NPO10467	Resupinatus leightonii	Species	Tricholomataceae	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	5

Activity Type	# Activity
Cell Line	3
NON-MOLECULAR	1
Organism	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT15	Cell Line	Jurkat	Homo sapiens	IC50	=	20.0	ug.mL-1	PMID[534809]
NPT116	Cell Line	HL-60	Homo sapiens	IC50	=	5.0	ug.mL-1	PMID[534809]
NPT165	Cell Line	HeLa	Homo sapiens	IC50	=	75.0	ug.mL-1	PMID[534809]
NPT1198	Organism	Magnaporthe grisea	Magnaporthe grisea	IC50	=	10.0	ug.mL-1	PMID[534809]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	IC50	=	75.0	ug.mL-1	PMID[534809]

☑ 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 NPC227135 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	134
0.1-0.2	2424
0.2-0.3	13257
0.3-0.4	15578
0.4-0.5	7740
0.5-0.6	2824
0.6-0.7	603
0.7-0.8	116
0.8-0.85	18
0.85-0.9	1
0.9-0.95	1
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
0.8889	High Similarity	NPC281590
0.8571	High Similarity	NPC52012
0.8448	Intermediate Similarity	NPC469694
0.8361	Intermediate Similarity	NPC267027
0.8276	Intermediate Similarity	NPC475931
0.8276	Intermediate Similarity	NPC278202
0.8103	Intermediate Similarity	NPC181872
0.8103	Intermediate Similarity	NPC155025
0.8033	Intermediate Similarity	NPC300593
0.8	Intermediate Similarity	NPC207007
0.8	Intermediate Similarity	NPC64971
0.8	Intermediate Similarity	NPC321867
0.8	Intermediate Similarity	NPC35756
0.8	Intermediate Similarity	NPC68679
0.7966	Intermediate Similarity	NPC122239
0.7963	Intermediate Similarity	NPC474460
0.7937	Intermediate Similarity	NPC82337
0.7903	Intermediate Similarity	NPC308844
0.7857	Intermediate Similarity	NPC474496
0.7833	Intermediate Similarity	NPC240506
0.7833	Intermediate Similarity	NPC99487
0.7833	Intermediate Similarity	NPC66020
0.7818	Intermediate Similarity	NPC473672
0.7818	Intermediate Similarity	NPC474495
0.7797	Intermediate Similarity	NPC226848
0.7778	Intermediate Similarity	NPC326310
0.7778	Intermediate Similarity	NPC311736
0.7759	Intermediate Similarity	NPC48891
0.7705	Intermediate Similarity	NPC225342
0.7692	Intermediate Similarity	NPC472947
0.7656	Intermediate Similarity	NPC73603
0.7656	Intermediate Similarity	NPC163290
0.7647	Intermediate Similarity	NPC249801
0.7647	Intermediate Similarity	NPC209279
0.7647	Intermediate Similarity	NPC51758
0.7647	Intermediate Similarity	NPC68889
0.7647	Intermediate Similarity	NPC180871
0.7647	Intermediate Similarity	NPC46248
0.7647	Intermediate Similarity	NPC67761
0.7647	Intermediate Similarity	NPC194586
0.7647	Intermediate Similarity	NPC108494
0.7647	Intermediate Similarity	NPC88079
0.7619	Intermediate Similarity	NPC471200
0.7586	Intermediate Similarity	NPC251666
0.7586	Intermediate Similarity	NPC329686
0.7586	Intermediate Similarity	NPC232247
0.7581	Intermediate Similarity	NPC473508
0.7547	Intermediate Similarity	NPC165651
0.7547	Intermediate Similarity	NPC24824
0.7547	Intermediate Similarity	NPC210560
0.7544	Intermediate Similarity	NPC217188
0.7541	Intermediate Similarity	NPC258788
0.75	Intermediate Similarity	NPC137163
0.75	Intermediate Similarity	NPC93639
0.7424	Intermediate Similarity	NPC473893
0.7419	Intermediate Similarity	NPC475251
0.7414	Intermediate Similarity	NPC110732
0.7414	Intermediate Similarity	NPC256209
0.7414	Intermediate Similarity	NPC49059
0.7385	Intermediate Similarity	NPC259299
0.7385	Intermediate Similarity	NPC473357
0.7385	Intermediate Similarity	NPC193029
0.7368	Intermediate Similarity	NPC294358
0.7368	Intermediate Similarity	NPC68014
0.7368	Intermediate Similarity	NPC40417
0.7344	Intermediate Similarity	NPC473722
0.7333	Intermediate Similarity	NPC121034
0.7321	Intermediate Similarity	NPC329773
0.7313	Intermediate Similarity	NPC129630
0.7302	Intermediate Similarity	NPC474155
0.7302	Intermediate Similarity	NPC473759
0.7288	Intermediate Similarity	NPC317899
0.7288	Intermediate Similarity	NPC148216
0.7288	Intermediate Similarity	NPC130209
0.7288	Intermediate Similarity	NPC148163
0.7273	Intermediate Similarity	NPC310210
0.7273	Intermediate Similarity	NPC305698
0.7273	Intermediate Similarity	NPC224532
0.7246	Intermediate Similarity	NPC190859
0.7231	Intermediate Similarity	NPC250977
0.7222	Intermediate Similarity	NPC140501
0.7213	Intermediate Similarity	NPC152438
0.7213	Intermediate Similarity	NPC41180
0.7206	Intermediate Similarity	NPC471268
0.7206	Intermediate Similarity	NPC471271
0.7193	Intermediate Similarity	NPC151782
0.7193	Intermediate Similarity	NPC26906
0.7193	Intermediate Similarity	NPC59408
0.7193	Intermediate Similarity	NPC71053
0.7193	Intermediate Similarity	NPC214584
0.7188	Intermediate Similarity	NPC309300
0.7188	Intermediate Similarity	NPC110241
0.717	Intermediate Similarity	NPC15162
0.717	Intermediate Similarity	NPC252978
0.7167	Intermediate Similarity	NPC24443
0.7164	Intermediate Similarity	NPC471560
0.7164	Intermediate Similarity	NPC16964
0.7164	Intermediate Similarity	NPC329989
0.7164	Intermediate Similarity	NPC239373
0.7143	Intermediate Similarity	NPC153538
0.7121	Intermediate Similarity	NPC477791
0.7121	Intermediate Similarity	NPC136813
0.7115	Intermediate Similarity	NPC188596
0.7097	Intermediate Similarity	NPC473866
0.7083	Intermediate Similarity	NPC475980
0.7077	Intermediate Similarity	NPC19569
0.7077	Intermediate Similarity	NPC250836
0.7077	Intermediate Similarity	NPC287339
0.7069	Intermediate Similarity	NPC179169
0.7069	Intermediate Similarity	NPC157781
0.7069	Intermediate Similarity	NPC306195
0.7069	Intermediate Similarity	NPC181255
0.7069	Intermediate Similarity	NPC35519
0.7042	Intermediate Similarity	NPC170148
0.7042	Intermediate Similarity	NPC126969
0.7042	Intermediate Similarity	NPC236228
0.7042	Intermediate Similarity	NPC256720
0.7018	Intermediate Similarity	NPC288381
0.7018	Intermediate Similarity	NPC20934
0.7018	Intermediate Similarity	NPC182102
0.7018	Intermediate Similarity	NPC26960
0.7018	Intermediate Similarity	NPC72699
0.7015	Intermediate Similarity	NPC117804
0.7015	Intermediate Similarity	NPC471238
0.7015	Intermediate Similarity	NPC272961
0.7015	Intermediate Similarity	NPC167527
0.7	Intermediate Similarity	NPC475353
0.7	Intermediate Similarity	NPC477726
0.7	Intermediate Similarity	NPC474644
0.7	Intermediate Similarity	NPC227814
0.7	Intermediate Similarity	NPC471525
0.7	Intermediate Similarity	NPC477725
0.7	Intermediate Similarity	NPC144995
0.7	Intermediate Similarity	NPC473896
0.7	Intermediate Similarity	NPC473735
0.7	Intermediate Similarity	NPC473721
0.7	Intermediate Similarity	NPC473725
0.7	Intermediate Similarity	NPC473910
0.6984	Remote Similarity	NPC471081
0.697	Remote Similarity	NPC202017
0.6957	Remote Similarity	NPC471272
0.6957	Remote Similarity	NPC41886
0.6957	Remote Similarity	NPC242992
0.6957	Remote Similarity	NPC23954
0.6949	Remote Similarity	NPC165755
0.6944	Remote Similarity	NPC40049
0.6944	Remote Similarity	NPC476703
0.6935	Remote Similarity	NPC475830
0.6923	Remote Similarity	NPC56917
0.6923	Remote Similarity	NPC96793
0.6923	Remote Similarity	NPC323424
0.6912	Remote Similarity	NPC217570
0.6912	Remote Similarity	NPC90115
0.6912	Remote Similarity	NPC304690
0.6912	Remote Similarity	NPC74722
0.6909	Remote Similarity	NPC87439
0.6909	Remote Similarity	NPC76976
0.6897	Remote Similarity	NPC129263
0.6897	Remote Similarity	NPC200772
0.6897	Remote Similarity	NPC244038
0.6897	Remote Similarity	NPC29234
0.6885	Remote Similarity	NPC477661
0.6885	Remote Similarity	NPC471960
0.6885	Remote Similarity	NPC470969
0.6885	Remote Similarity	NPC475384
0.6885	Remote Similarity	NPC470968
0.6885	Remote Similarity	NPC470967
0.6885	Remote Similarity	NPC473847
0.6885	Remote Similarity	NPC470966
0.6885	Remote Similarity	NPC474643
0.6885	Remote Similarity	NPC161838
0.6885	Remote Similarity	NPC473865
0.6875	Remote Similarity	NPC274704
0.6875	Remote Similarity	NPC55376
0.6866	Remote Similarity	NPC114651
0.6866	Remote Similarity	NPC472255
0.6866	Remote Similarity	NPC472253
0.6863	Remote Similarity	NPC40434
0.6863	Remote Similarity	NPC34873
0.6857	Remote Similarity	NPC329763
0.6857	Remote Similarity	NPC220939
0.6857	Remote Similarity	NPC265485
0.6857	Remote Similarity	NPC130665
0.6857	Remote Similarity	NPC476709
0.6852	Remote Similarity	NPC116934
0.6849	Remote Similarity	NPC167891
0.6849	Remote Similarity	NPC83351
0.6842	Remote Similarity	NPC248884
0.6842	Remote Similarity	NPC31194
0.6842	Remote Similarity	NPC302310
0.6842	Remote Similarity	NPC85079
0.6833	Remote Similarity	NPC473532
0.6825	Remote Similarity	NPC83838
0.6825	Remote Similarity	NPC143810
0.6818	Remote Similarity	NPC61503
0.6812	Remote Similarity	NPC473361
0.6812	Remote Similarity	NPC189745
0.6812	Remote Similarity	NPC4299
0.6812	Remote Similarity	NPC329904
0.6812	Remote Similarity	NPC471781

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 NPC227135 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	135
0.1-0.2	2786
0.2-0.3	4090
0.3-0.4	1652
0.4-0.5	365
0.5-0.6	108
0.6-0.7	10
0.7-0.8	3
0.8-0.85	1
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8	Intermediate Similarity	NPD368	Approved
0.7288	Intermediate Similarity	NPD342	Phase 1
0.7222	Intermediate Similarity	NPD4265	Approved
0.6857	Remote Similarity	NPD4732	Discontinued
0.6719	Remote Similarity	NPD4246	Clinical (unspecified phase)
0.6667	Remote Similarity	NPD8264	Approved
0.6622	Remote Similarity	NPD7322	Clinical (unspecified phase)
0.6613	Remote Similarity	NPD4219	Approved
0.6575	Remote Similarity	NPD6933	Approved
0.6447	Remote Similarity	NPD7514	Phase 3
0.6447	Remote Similarity	NPD7332	Phase 2
0.6418	Remote Similarity	NPD3197	Phase 1
0.6406	Remote Similarity	NPD585	Clinical (unspecified phase)
0.64	Remote Similarity	NPD7145	Approved
0.6338	Remote Similarity	NPD7143	Approved
0.6338	Remote Similarity	NPD7144	Approved
0.6324	Remote Similarity	NPD2685	Clinical (unspecified phase)
0.6301	Remote Similarity	NPD6924	Approved
0.6301	Remote Similarity	NPD6926	Approved
0.6267	Remote Similarity	NPD5776	Phase 2
0.6267	Remote Similarity	NPD6925	Approved
0.6267	Remote Similarity	NPD6932	Approved
0.625	Remote Similarity	NPD7152	Approved
0.625	Remote Similarity	NPD7150	Approved
0.625	Remote Similarity	NPD7151	Approved
0.6234	Remote Similarity	NPD4821	Approved
0.6234	Remote Similarity	NPD6931	Approved
0.6234	Remote Similarity	NPD4822	Approved
0.6234	Remote Similarity	NPD6930	Phase 2
0.6234	Remote Similarity	NPD4819	Approved
0.6234	Remote Similarity	NPD4820	Approved
0.6197	Remote Similarity	NPD6923	Approved
0.6197	Remote Similarity	NPD6922	Approved
0.6184	Remote Similarity	NPD5784	Clinical (unspecified phase)
0.6154	Remote Similarity	NPD6902	Approved
0.6154	Remote Similarity	NPD6898	Phase 1
0.6104	Remote Similarity	NPD6929	Approved
0.6098	Remote Similarity	NPD7524	Approved
0.6029	Remote Similarity	NPD3210	Clinical (unspecified phase)
0.6	Remote Similarity	NPD5332	Approved
0.6	Remote Similarity	NPD6695	Phase 3
0.6	Remote Similarity	NPD7154	Phase 3
0.6	Remote Similarity	NPD5362	Discontinued
0.6	Remote Similarity	NPD7331	Phase 2
0.6	Remote Similarity	NPD5331	Approved
0.5974	Remote Similarity	NPD4268	Approved
0.5974	Remote Similarity	NPD4271	Approved
0.5949	Remote Similarity	NPD4790	Discontinued
0.5926	Remote Similarity	NPD7338	Clinical (unspecified phase)
0.5921	Remote Similarity	NPD3701	Clinical (unspecified phase)
0.5915	Remote Similarity	NPD4247	Clinical (unspecified phase)
0.5909	Remote Similarity	NPD6109	Phase 1
0.5897	Remote Similarity	NPD6683	Phase 2
0.5875	Remote Similarity	NPD4269	Approved
0.5875	Remote Similarity	NPD4270	Approved
0.5854	Remote Similarity	NPD6893	Approved
0.5823	Remote Similarity	NPD4252	Approved
0.5823	Remote Similarity	NPD7509	Discontinued
0.5823	Remote Similarity	NPD7525	Registered
0.5823	Remote Similarity	NPD5790	Clinical (unspecified phase)
0.5814	Remote Similarity	NPD7983	Approved
0.5802	Remote Similarity	NPD6110	Phase 1
0.5789	Remote Similarity	NPD6942	Approved
0.5789	Remote Similarity	NPD7339	Approved
0.575	Remote Similarity	NPD5369	Approved
0.5738	Remote Similarity	NPD3173	Approved
0.5714	Remote Similarity	NPD7750	Discontinued
0.5714	Remote Similarity	NPD4751	Clinical (unspecified phase)
0.5698	Remote Similarity	NPD7838	Discovery
0.5696	Remote Similarity	NPD7645	Phase 2
0.5663	Remote Similarity	NPD5363	Approved
0.5652	Remote Similarity	NPD4194	Approved
0.5652	Remote Similarity	NPD4193	Approved
0.5652	Remote Similarity	NPD4191	Approved
0.5652	Remote Similarity	NPD4192	Approved
0.5625	Remote Similarity	NPD3172	Approved
0.5625	Remote Similarity	NPD8259	Clinical (unspecified phase)
0.5625	Remote Similarity	NPD5368	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