NPASS Compound

Structure

Physi-Chem Properties

Molecular Weight:	256.2
Volume:	277.254
LogP:	2.877
LogD:	3.207
LogS:	-3.372
# Rotatable Bonds:	1
TPSA:	60.69
# H-Bond Aceptor:	3
# H-Bond Donor:	3
# Rings:	2
# Heavy Atoms:	3

MedChem Properties

QED Drug-Likeness Score:	0.672
Synthetic Accessibility Score:	4.455
Fsp3:	1.0
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:	-4.601
MDCK Permeability:	1.181457810162101e-05
Pgp-inhibitor:	0.001
Pgp-substrate:	0.952
Human Intestinal Absorption (HIA):	0.01
20% Bioavailability (F20%):	0.887
30% Bioavailability (F30%):	0.023

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.807
Plasma Protein Binding (PPB):	69.53426361083984%
Volume Distribution (VD):	0.877
Pgp-substrate:	22.098806381225586%

ADMET: Metabolism

CYP1A2-inhibitor:	0.111
CYP1A2-substrate:	0.138
CYP2C19-inhibitor:	0.019
CYP2C19-substrate:	0.806
CYP2C9-inhibitor:	0.053
CYP2C9-substrate:	0.169
CYP2D6-inhibitor:	0.004
CYP2D6-substrate:	0.125
CYP3A4-inhibitor:	0.031
CYP3A4-substrate:	0.261

ADMET: Excretion

Clearance (CL):	8.765
Half-life (T1/2):	0.613

ADMET: Toxicity

hERG Blockers:	0.061
Human Hepatotoxicity (H-HT):	0.178
Drug-inuced Liver Injury (DILI):	0.193
AMES Toxicity:	0.037
Rat Oral Acute Toxicity:	0.939
Maximum Recommended Daily Dose:	0.78
Skin Sensitization:	0.881
Carcinogencity:	0.861
Eye Corrosion:	0.917
Eye Irritation:	0.898
Respiratory Toxicity:	0.965

Download Data

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

Natural Product: NPC47663

Natural Product ID:	NPC47663
*Common Name:**	4Alpha-Methylcadinane-1Alpha,2Alpha,10Alpha Triol
IUPAC Name:	(1S,3S,4aS,5S,8R,8aR)-3,8-dimethyl-5-propan-2-yl-1,2,3,4,4a,5,6,7-octahydronaphthalene-1,8,8a-triol
Synonyms:	4Alpha-Methylcadinane-1Alpha,2Alpha,10Alpha Triol
Standard InCHIKey:	NOMPOPNILJKBDF-GXYBRJDSSA-N
Standard InCHI:	InChI=1S/C15H28O3/c1-9(2)11-5-6-14(4,17)15(18)12(11)7-10(3)8-13(15)16/h9-13,16-18H,5-8H2,1-4H3/t10-,11-,12-,13-,14+,15+/m0/s1
SMILES:	C[C@@H]1C[C@H](O)[C@@]2([C@@H](C1)[C@@H](CC[C@@]2(C)O)C(C)C)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL504739
PubChem CID:	10801091
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
NPO24241	Taiwania cryptomerioides	Species	Cupressaceae	Eukaryota	n.a.	twig	n.a.	PMID[22474975]
NPO24241	Taiwania cryptomerioides	Species	Cupressaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[31347365]
NPO24241	Taiwania cryptomerioides	Species	Cupressaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[9014350]
NPO24241	Taiwania cryptomerioides	Species	Cupressaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO24241	Taiwania cryptomerioides	Species	Cupressaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO24241	Taiwania cryptomerioides	Species	Cupressaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO24241	Taiwania cryptomerioides	Species	Cupressaceae	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
ED50	3
Others	2

Activity Type	# Activity
Cell Line	3
Organism	2

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT81	Cell Line	A549	Homo sapiens	ED50	=	13.34	ug ml-1	PMID[515229]
NPT83	Cell Line	MCF7	Homo sapiens	ED50	=	41.05	ug ml-1	PMID[515229]
NPT139	Cell Line	HT-29	Homo sapiens	ED50	=	12.01	ug ml-1	PMID[515229]
NPT176	Organism	Artemia salina	Artemia salina	LC50	=	84.8	ug.mL-1	PMID[515229]
NPT1381	Organism	Aedes aegypti	Aedes aegypti	LC50	>	250.0	ug.mL-1	PMID[515229]

☑ 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 NPC47663 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	420
0.1-0.2	4423
0.2-0.3	15655
0.3-0.4	11339
0.4-0.5	6245
0.5-0.6	3621
0.6-0.7	831
0.7-0.8	149
0.8-0.85	8
0.85-0.9	3
0.9-0.95	2
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
0.9153	High Similarity	NPC94897
0.8475	Intermediate Similarity	NPC185116
0.8448	Intermediate Similarity	NPC135438
0.8448	Intermediate Similarity	NPC236588
0.8438	Intermediate Similarity	NPC470833
0.8387	Intermediate Similarity	NPC260116
0.8281	Intermediate Similarity	NPC244790
0.8281	Intermediate Similarity	NPC475893
0.8154	Intermediate Similarity	NPC107919
0.8125	Intermediate Similarity	NPC204233
0.8103	Intermediate Similarity	NPC471269
0.803	Intermediate Similarity	NPC231945
0.7963	Intermediate Similarity	NPC198540
0.7963	Intermediate Similarity	NPC147343
0.7963	Intermediate Similarity	NPC84030
0.7963	Intermediate Similarity	NPC287550
0.7963	Intermediate Similarity	NPC223468
0.7963	Intermediate Similarity	NPC176309
0.7941	Intermediate Similarity	NPC192501
0.7941	Intermediate Similarity	NPC10476
0.7941	Intermediate Similarity	NPC470151
0.7941	Intermediate Similarity	NPC228994
0.7931	Intermediate Similarity	NPC53209
0.7903	Intermediate Similarity	NPC95804
0.7903	Intermediate Similarity	NPC185547
0.7879	Intermediate Similarity	NPC299948
0.7879	Intermediate Similarity	NPC470830
0.7879	Intermediate Similarity	NPC241085
0.7826	Intermediate Similarity	NPC158208
0.7826	Intermediate Similarity	NPC243027
0.7826	Intermediate Similarity	NPC196136
0.7812	Intermediate Similarity	NPC472946
0.7812	Intermediate Similarity	NPC80463
0.7794	Intermediate Similarity	NPC95165
0.7759	Intermediate Similarity	NPC36002
0.7759	Intermediate Similarity	NPC102336
0.7727	Intermediate Similarity	NPC474756
0.7714	Intermediate Similarity	NPC163597
0.7679	Intermediate Similarity	NPC316035
0.7656	Intermediate Similarity	NPC101128
0.7647	Intermediate Similarity	NPC131506
0.7647	Intermediate Similarity	NPC242992
0.7647	Intermediate Similarity	NPC157777
0.7606	Intermediate Similarity	NPC105208
0.7606	Intermediate Similarity	NPC477227
0.7606	Intermediate Similarity	NPC128951
0.7606	Intermediate Similarity	NPC192046
0.7606	Intermediate Similarity	NPC302578
0.7576	Intermediate Similarity	NPC63190
0.7576	Intermediate Similarity	NPC269077
0.7576	Intermediate Similarity	NPC139207
0.7576	Intermediate Similarity	NPC48079
0.7576	Intermediate Similarity	NPC475884
0.7576	Intermediate Similarity	NPC253303
0.7576	Intermediate Similarity	NPC185874
0.7576	Intermediate Similarity	NPC473230
0.7571	Intermediate Similarity	NPC472950
0.7571	Intermediate Similarity	NPC472952
0.7571	Intermediate Similarity	NPC317242
0.7536	Intermediate Similarity	NPC473238
0.7536	Intermediate Similarity	NPC472341
0.7536	Intermediate Similarity	NPC153719
0.75	Intermediate Similarity	NPC314087
0.75	Intermediate Similarity	NPC147993
0.75	Intermediate Similarity	NPC236099
0.75	Intermediate Similarity	NPC209686
0.75	Intermediate Similarity	NPC18857
0.75	Intermediate Similarity	NPC249078
0.75	Intermediate Similarity	NPC292419
0.75	Intermediate Similarity	NPC114891
0.75	Intermediate Similarity	NPC290791
0.75	Intermediate Similarity	NPC67657
0.75	Intermediate Similarity	NPC52755
0.7465	Intermediate Similarity	NPC470145
0.7463	Intermediate Similarity	NPC472741
0.7463	Intermediate Similarity	NPC469987
0.7463	Intermediate Similarity	NPC276616
0.7463	Intermediate Similarity	NPC266578
0.7424	Intermediate Similarity	NPC142712
0.7424	Intermediate Similarity	NPC44122
0.7419	Intermediate Similarity	NPC475515
0.7419	Intermediate Similarity	NPC87296
0.7419	Intermediate Similarity	NPC215671
0.7414	Intermediate Similarity	NPC307022
0.7407	Intermediate Similarity	NPC144891
0.7397	Intermediate Similarity	NPC269333
0.7391	Intermediate Similarity	NPC127283
0.7391	Intermediate Similarity	NPC8004
0.7385	Intermediate Similarity	NPC167995
0.7385	Intermediate Similarity	NPC159654
0.7385	Intermediate Similarity	NPC144650
0.7385	Intermediate Similarity	NPC281540
0.7385	Intermediate Similarity	NPC118937
0.7361	Intermediate Similarity	NPC11907
0.7361	Intermediate Similarity	NPC133596
0.7361	Intermediate Similarity	NPC185915
0.7353	Intermediate Similarity	NPC254037
0.7353	Intermediate Similarity	NPC210323
0.7353	Intermediate Similarity	NPC129829
0.7353	Intermediate Similarity	NPC66407
0.7353	Intermediate Similarity	NPC234511
0.7344	Intermediate Similarity	NPC71460
0.7344	Intermediate Similarity	NPC218585
0.7344	Intermediate Similarity	NPC148174
0.7324	Intermediate Similarity	NPC91387
0.7324	Intermediate Similarity	NPC231680
0.7324	Intermediate Similarity	NPC270306
0.7321	Intermediate Similarity	NPC14552
0.7313	Intermediate Similarity	NPC476928
0.7297	Intermediate Similarity	NPC16449
0.7297	Intermediate Similarity	NPC186588
0.7288	Intermediate Similarity	NPC476136
0.7288	Intermediate Similarity	NPC476149
0.7288	Intermediate Similarity	NPC244869
0.7288	Intermediate Similarity	NPC300235
0.7286	Intermediate Similarity	NPC470610
0.7286	Intermediate Similarity	NPC81759
0.7286	Intermediate Similarity	NPC253805
0.7273	Intermediate Similarity	NPC190827
0.7273	Intermediate Similarity	NPC282619
0.7273	Intermediate Similarity	NPC208198
0.7273	Intermediate Similarity	NPC2728
0.7273	Intermediate Similarity	NPC172613
0.7273	Intermediate Similarity	NPC11555
0.7273	Intermediate Similarity	NPC243469
0.7273	Intermediate Similarity	NPC473276
0.7273	Intermediate Similarity	NPC60837
0.7273	Intermediate Similarity	NPC475943
0.7273	Intermediate Similarity	NPC258595
0.7273	Intermediate Similarity	NPC474380
0.7273	Intermediate Similarity	NPC41577
0.7246	Intermediate Similarity	NPC283316
0.7246	Intermediate Similarity	NPC282454
0.7246	Intermediate Similarity	NPC192192
0.7222	Intermediate Similarity	NPC477602
0.7222	Intermediate Similarity	NPC91573
0.7222	Intermediate Similarity	NPC477601
0.7222	Intermediate Similarity	NPC473916
0.7206	Intermediate Similarity	NPC245795
0.7206	Intermediate Similarity	NPC2648
0.72	Intermediate Similarity	NPC470156
0.7183	Intermediate Similarity	NPC166250
0.7183	Intermediate Similarity	NPC304499
0.7183	Intermediate Similarity	NPC48795
0.7183	Intermediate Similarity	NPC475458
0.7164	Intermediate Similarity	NPC473929
0.7162	Intermediate Similarity	NPC287452
0.7162	Intermediate Similarity	NPC81074
0.7162	Intermediate Similarity	NPC477282
0.7143	Intermediate Similarity	NPC195530
0.7143	Intermediate Similarity	NPC252182
0.7143	Intermediate Similarity	NPC109457
0.7143	Intermediate Similarity	NPC157422
0.7143	Intermediate Similarity	NPC473279
0.7143	Intermediate Similarity	NPC167706
0.7143	Intermediate Similarity	NPC187471
0.7143	Intermediate Similarity	NPC1340
0.7143	Intermediate Similarity	NPC108441
0.7143	Intermediate Similarity	NPC470071
0.7143	Intermediate Similarity	NPC127094
0.7143	Intermediate Similarity	NPC77550
0.7143	Intermediate Similarity	NPC100586
0.7123	Intermediate Similarity	NPC64081
0.7123	Intermediate Similarity	NPC474574
0.7121	Intermediate Similarity	NPC68656
0.7121	Intermediate Similarity	NPC69149
0.7105	Intermediate Similarity	NPC470155
0.7105	Intermediate Similarity	NPC60018
0.7105	Intermediate Similarity	NPC477446
0.7105	Intermediate Similarity	NPC477447
0.7105	Intermediate Similarity	NPC202688
0.7105	Intermediate Similarity	NPC154043
0.7101	Intermediate Similarity	NPC99264
0.7101	Intermediate Similarity	NPC477820
0.7097	Intermediate Similarity	NPC3025
0.7067	Intermediate Similarity	NPC472943
0.7067	Intermediate Similarity	NPC472951
0.7059	Intermediate Similarity	NPC472984
0.7042	Intermediate Similarity	NPC265485
0.7042	Intermediate Similarity	NPC220939
0.7031	Intermediate Similarity	NPC95958
0.7027	Intermediate Similarity	NPC177343
0.7027	Intermediate Similarity	NPC102708
0.7013	Intermediate Similarity	NPC477978
0.7013	Intermediate Similarity	NPC216420
0.7013	Intermediate Similarity	NPC241959
0.7013	Intermediate Similarity	NPC478054
0.7013	Intermediate Similarity	NPC85095
0.7013	Intermediate Similarity	NPC211135
0.7	Intermediate Similarity	NPC251201
0.7	Intermediate Similarity	NPC63588
0.7	Intermediate Similarity	NPC232925
0.6986	Remote Similarity	NPC63958
0.6986	Remote Similarity	NPC470766
0.6986	Remote Similarity	NPC136424
0.6974	Remote Similarity	NPC470154
0.6964	Remote Similarity	NPC313795
0.6964	Remote Similarity	NPC240994
0.6957	Remote Similarity	NPC478228
0.6944	Remote Similarity	NPC475793

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 NPC47663 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	478
0.1-0.2	4378
0.2-0.3	2918
0.3-0.4	909
0.4-0.5	305
0.5-0.6	128
0.6-0.7	30
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
0.8226	Intermediate Similarity	NPD371	Approved
0.8154	Intermediate Similarity	NPD4267	Clinical (unspecified phase)
0.7963	Intermediate Similarity	NPD384	Approved
0.7963	Intermediate Similarity	NPD385	Approved
0.7143	Intermediate Similarity	NPD388	Approved
0.7143	Intermediate Similarity	NPD386	Approved
0.7	Intermediate Similarity	NPD4787	Phase 1
0.6857	Remote Similarity	NPD3700	Clinical (unspecified phase)
0.6857	Remote Similarity	NPD3699	Clinical (unspecified phase)
0.6667	Remote Similarity	NPD4808	Clinical (unspecified phase)
0.6667	Remote Similarity	NPD4809	Clinical (unspecified phase)
0.6622	Remote Similarity	NPD3703	Phase 2
0.6533	Remote Similarity	NPD6117	Approved
0.6522	Remote Similarity	NPD3171	Clinical (unspecified phase)
0.6494	Remote Similarity	NPD7645	Phase 2
0.6486	Remote Similarity	NPD1811	Approved
0.6486	Remote Similarity	NPD6113	Clinical (unspecified phase)
0.6486	Remote Similarity	NPD1810	Approved
0.6447	Remote Similarity	NPD6116	Phase 1
0.641	Remote Similarity	NPD7525	Registered
0.6389	Remote Similarity	NPD3698	Phase 2
0.6364	Remote Similarity	NPD6114	Approved
0.6364	Remote Similarity	NPD6118	Approved
0.6364	Remote Similarity	NPD6697	Approved
0.6364	Remote Similarity	NPD6115	Approved
0.6301	Remote Similarity	NPD7532	Clinical (unspecified phase)
0.6301	Remote Similarity	NPD4244	Approved
0.6301	Remote Similarity	NPD4245	Approved
0.625	Remote Similarity	NPD5361	Clinical (unspecified phase)
0.625	Remote Similarity	NPD5360	Phase 3
0.6207	Remote Similarity	NPD367	Approved
0.6154	Remote Similarity	NPD3671	Phase 1
0.6104	Remote Similarity	NPD3701	Clinical (unspecified phase)
0.6104	Remote Similarity	NPD6933	Approved
0.6081	Remote Similarity	NPD4789	Approved
0.6027	Remote Similarity	NPD6705	Phase 1
0.6	Remote Similarity	NPD6928	Phase 2
0.6	Remote Similarity	NPD4748	Discontinued
0.6	Remote Similarity	NPD4758	Discontinued
0.5974	Remote Similarity	NPD7339	Approved
0.5974	Remote Similarity	NPD6942	Approved
0.5867	Remote Similarity	NPD2254	Approved
0.5867	Remote Similarity	NPD2686	Approved
0.5867	Remote Similarity	NPD2687	Approved
0.5844	Remote Similarity	NPD6926	Approved
0.5844	Remote Similarity	NPD6924	Approved
0.5833	Remote Similarity	NPD7520	Clinical (unspecified phase)
0.5806	Remote Similarity	NPD4159	Approved
0.5769	Remote Similarity	NPD3702	Approved
0.5765	Remote Similarity	NPD3618	Phase 1
0.5763	Remote Similarity	NPD1462	Approved
0.5753	Remote Similarity	NPD4224	Phase 2
0.573	Remote Similarity	NPD8171	Discontinued
0.5698	Remote Similarity	NPD7524	Approved
0.569	Remote Similarity	NPD1460	Approved
0.5663	Remote Similarity	NPD3667	Approved
0.5634	Remote Similarity	NPD368	Approved
0.561	Remote Similarity	NPD6930	Phase 2
0.561	Remote Similarity	NPD6931	Approved
0.561	Remote Similarity	NPD7509	Discontinued

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