NPASS Compound

Structure

Physi-Chem Properties

Molecular Weight:	256.2
Volume:	277.254
LogP:	2.643
LogD:	2.849
LogS:	-3.508
# 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:	4.531
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:	-4.398
MDCK Permeability:	2.5809771614149213e-05
Pgp-inhibitor:	0.0
Pgp-substrate:	0.572
Human Intestinal Absorption (HIA):	0.009
20% Bioavailability (F20%):	0.872
30% Bioavailability (F30%):	0.226

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.374
Plasma Protein Binding (PPB):	92.29285430908203%
Volume Distribution (VD):	0.906
Pgp-substrate:	6.065098762512207%

ADMET: Metabolism

CYP1A2-inhibitor:	0.042
CYP1A2-substrate:	0.223
CYP2C19-inhibitor:	0.015
CYP2C19-substrate:	0.773
CYP2C9-inhibitor:	0.028
CYP2C9-substrate:	0.167
CYP2D6-inhibitor:	0.004
CYP2D6-substrate:	0.127
CYP3A4-inhibitor:	0.066
CYP3A4-substrate:	0.292

ADMET: Excretion

Clearance (CL):	7.209
Half-life (T1/2):	0.499

ADMET: Toxicity

hERG Blockers:	0.051
Human Hepatotoxicity (H-HT):	0.054
Drug-inuced Liver Injury (DILI):	0.044
AMES Toxicity:	0.007
Rat Oral Acute Toxicity:	0.258
Maximum Recommended Daily Dose:	0.014
Skin Sensitization:	0.289
Carcinogencity:	0.03
Eye Corrosion:	0.098
Eye Irritation:	0.31
Respiratory Toxicity:	0.846

Download Data

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

Natural Product: NPC94897

Natural Product ID:	NPC94897
*Common Name:**	(-)-(1R,4R,5S,6R,7S,10R)-Cadinan-1,4,5-Triol
IUPAC Name:	(1S,2R,4aR,5R,8S,8aR)-2,5-dimethyl-8-propan-2-yl-1,3,4,5,6,7,8,8a-octahydronaphthalene-1,2,4a-triol
Synonyms:
Standard InCHIKey:	NYZINEQQHFXDCC-ARSDKDGVSA-N
Standard InCHI:	InChI=1S/C15H28O3/c1-9(2)11-6-5-10(3)15(18)8-7-14(4,17)13(16)12(11)15/h9-13,16-18H,5-8H2,1-4H3/t10-,11+,12-,13+,14-,15-/m1/s1
SMILES:	CC(C)[C@@H]1CC[C@@H](C)[C@@]2(CC[C@](C)([C@H]([C@@H]12)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL462750
PubChem CID:	21589754
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
NPO29315	Dictyopteris divaricata	Species	Dictyotaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15497933]
NPO29315	Dictyopteris divaricata	Species	Dictyotaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[16180804]
NPO29315	Dictyopteris divaricata	Species	Dictyotaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[16989516]
NPO29315	Dictyopteris divaricata	Species	Dictyotaceae	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	5

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT81	Cell Line	A549	Homo sapiens	IC50	>	10.0	ug.mL-1	PMID[455252]
NPT547	Cell Line	BGC-823	Homo sapiens	IC50	>	10.0	ug.mL-1	PMID[455252]
NPT83	Cell Line	MCF7	Homo sapiens	IC50	>	10.0	ug.mL-1	PMID[455252]
NPT181	Cell Line	Bel-7402	Homo sapiens	IC50	>	10.0	ug.mL-1	PMID[455252]
NPT180	Cell Line	HCT-8	Homo sapiens	IC50	>	10.0	ug.mL-1	PMID[455252]

☑ 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 NPC94897 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	473
0.1-0.2	4551
0.2-0.3	12900
0.3-0.4	13622
0.4-0.5	6103
0.5-0.6	4107
0.6-0.7	785
0.7-0.8	138
0.8-0.85	11
0.85-0.9	4
0.9-0.95	2
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
0.9153	High Similarity	NPC47663
0.8676	High Similarity	NPC470151
0.8636	High Similarity	NPC470833
0.8406	Intermediate Similarity	NPC228994
0.8406	Intermediate Similarity	NPC10476
0.8406	Intermediate Similarity	NPC192501
0.8286	Intermediate Similarity	NPC158208
0.8286	Intermediate Similarity	NPC243027
0.8286	Intermediate Similarity	NPC196136
0.8194	Intermediate Similarity	NPC147993
0.8136	Intermediate Similarity	NPC476149
0.8136	Intermediate Similarity	NPC244869
0.8136	Intermediate Similarity	NPC300235
0.8136	Intermediate Similarity	NPC476136
0.8095	Intermediate Similarity	NPC185116
0.8065	Intermediate Similarity	NPC236588
0.8056	Intermediate Similarity	NPC105208
0.8056	Intermediate Similarity	NPC128951
0.8056	Intermediate Similarity	NPC477227
0.8056	Intermediate Similarity	NPC192046
0.8056	Intermediate Similarity	NPC302578
0.8033	Intermediate Similarity	NPC471269
0.8	Intermediate Similarity	NPC95165
0.7945	Intermediate Similarity	NPC18857
0.7945	Intermediate Similarity	NPC67657
0.7941	Intermediate Similarity	NPC474756
0.7917	Intermediate Similarity	NPC163597
0.7867	Intermediate Similarity	NPC470156
0.7838	Intermediate Similarity	NPC269333
0.7826	Intermediate Similarity	NPC234511
0.7808	Intermediate Similarity	NPC185915
0.7778	Intermediate Similarity	NPC472952
0.7778	Intermediate Similarity	NPC135438
0.7778	Intermediate Similarity	NPC317242
0.7778	Intermediate Similarity	NPC472950
0.7763	Intermediate Similarity	NPC470155
0.7763	Intermediate Similarity	NPC477446
0.7763	Intermediate Similarity	NPC477447
0.7761	Intermediate Similarity	NPC260116
0.7733	Intermediate Similarity	NPC186588
0.7733	Intermediate Similarity	NPC16449
0.7705	Intermediate Similarity	NPC102336
0.7705	Intermediate Similarity	NPC36002
0.7703	Intermediate Similarity	NPC52755
0.7681	Intermediate Similarity	NPC266578
0.7681	Intermediate Similarity	NPC475893
0.7681	Intermediate Similarity	NPC469987
0.7681	Intermediate Similarity	NPC244790
0.7662	Intermediate Similarity	NPC241959
0.7662	Intermediate Similarity	NPC478054
0.7639	Intermediate Similarity	NPC475458
0.7639	Intermediate Similarity	NPC304499
0.7632	Intermediate Similarity	NPC470154
0.76	Intermediate Similarity	NPC81074
0.76	Intermediate Similarity	NPC477282
0.76	Intermediate Similarity	NPC287452
0.7571	Intermediate Similarity	NPC107919
0.7571	Intermediate Similarity	NPC66407
0.7564	Intermediate Similarity	NPC320824
0.7536	Intermediate Similarity	NPC179823
0.7536	Intermediate Similarity	NPC185874
0.7536	Intermediate Similarity	NPC269077
0.7536	Intermediate Similarity	NPC253303
0.7536	Intermediate Similarity	NPC204233
0.7536	Intermediate Similarity	NPC139207
0.7532	Intermediate Similarity	NPC202688
0.7532	Intermediate Similarity	NPC154043
0.7532	Intermediate Similarity	NPC60018
0.75	Intermediate Similarity	NPC472946
0.75	Intermediate Similarity	NPC470610
0.75	Intermediate Similarity	NPC153719
0.7465	Intermediate Similarity	NPC283316
0.7465	Intermediate Similarity	NPC231945
0.7463	Intermediate Similarity	NPC236099
0.7463	Intermediate Similarity	NPC209686
0.7463	Intermediate Similarity	NPC249078
0.7436	Intermediate Similarity	NPC85095
0.7436	Intermediate Similarity	NPC216420
0.7436	Intermediate Similarity	NPC211135
0.7432	Intermediate Similarity	NPC63958
0.7397	Intermediate Similarity	NPC166250
0.7397	Intermediate Similarity	NPC48795
0.7385	Intermediate Similarity	NPC476209
0.7385	Intermediate Similarity	NPC475515
0.7385	Intermediate Similarity	NPC87296
0.7385	Intermediate Similarity	NPC215671
0.7361	Intermediate Similarity	NPC252182
0.7361	Intermediate Similarity	NPC187471
0.7361	Intermediate Similarity	NPC1340
0.7361	Intermediate Similarity	NPC470071
0.7361	Intermediate Similarity	NPC127094
0.7333	Intermediate Similarity	NPC11907
0.7333	Intermediate Similarity	NPC133596
0.7333	Intermediate Similarity	NPC64081
0.7333	Intermediate Similarity	NPC474574
0.7324	Intermediate Similarity	NPC299948
0.7324	Intermediate Similarity	NPC241085
0.7324	Intermediate Similarity	NPC470830
0.7324	Intermediate Similarity	NPC254037
0.7324	Intermediate Similarity	NPC477820
0.7324	Intermediate Similarity	NPC129829
0.7313	Intermediate Similarity	NPC95804
0.7313	Intermediate Similarity	NPC185547
0.7302	Intermediate Similarity	NPC53209
0.7297	Intermediate Similarity	NPC231680
0.7297	Intermediate Similarity	NPC270306
0.7297	Intermediate Similarity	NPC91387
0.7288	Intermediate Similarity	NPC176309
0.7288	Intermediate Similarity	NPC198540
0.7288	Intermediate Similarity	NPC84030
0.7288	Intermediate Similarity	NPC223468
0.7288	Intermediate Similarity	NPC147343
0.7288	Intermediate Similarity	NPC287550
0.7284	Intermediate Similarity	NPC110365
0.7284	Intermediate Similarity	NPC213658
0.7284	Intermediate Similarity	NPC62202
0.7284	Intermediate Similarity	NPC45833
0.7273	Intermediate Similarity	NPC95124
0.7273	Intermediate Similarity	NPC471266
0.7273	Intermediate Similarity	NPC472951
0.7273	Intermediate Similarity	NPC472943
0.726	Intermediate Similarity	NPC253805
0.725	Intermediate Similarity	NPC266651
0.7246	Intermediate Similarity	NPC80463
0.7237	Intermediate Similarity	NPC43463
0.7237	Intermediate Similarity	NPC177343
0.7237	Intermediate Similarity	NPC471769
0.7237	Intermediate Similarity	NPC272841
0.7222	Intermediate Similarity	NPC63588
0.7222	Intermediate Similarity	NPC232925
0.7222	Intermediate Similarity	NPC192192
0.7222	Intermediate Similarity	NPC251201
0.7215	Intermediate Similarity	NPC477978
0.72	Intermediate Similarity	NPC136424
0.72	Intermediate Similarity	NPC477601
0.72	Intermediate Similarity	NPC473916
0.72	Intermediate Similarity	NPC477602
0.7195	Intermediate Similarity	NPC476379
0.7183	Intermediate Similarity	NPC472741
0.7183	Intermediate Similarity	NPC245795
0.7179	Intermediate Similarity	NPC211049
0.7179	Intermediate Similarity	NPC471270
0.716	Intermediate Similarity	NPC121981
0.716	Intermediate Similarity	NPC268633
0.716	Intermediate Similarity	NPC474215
0.716	Intermediate Similarity	NPC475729
0.7143	Intermediate Similarity	NPC44122
0.7123	Intermediate Similarity	NPC131506
0.7123	Intermediate Similarity	NPC242992
0.7123	Intermediate Similarity	NPC157777
0.7121	Intermediate Similarity	NPC182903
0.7119	Intermediate Similarity	NPC77550
0.7119	Intermediate Similarity	NPC108441
0.7105	Intermediate Similarity	NPC476233
0.7101	Intermediate Similarity	NPC101128
0.7097	Intermediate Similarity	NPC307022
0.7089	Intermediate Similarity	NPC475388
0.7073	Intermediate Similarity	NPC5943
0.7073	Intermediate Similarity	NPC263802
0.7067	Intermediate Similarity	NPC131584
0.7067	Intermediate Similarity	NPC139765
0.7051	Intermediate Similarity	NPC186594
0.7051	Intermediate Similarity	NPC236707
0.7049	Intermediate Similarity	NPC316035
0.7042	Intermediate Similarity	NPC48079
0.7042	Intermediate Similarity	NPC476928
0.7042	Intermediate Similarity	NPC473230
0.7042	Intermediate Similarity	NPC63190
0.7042	Intermediate Similarity	NPC475884
0.7027	Intermediate Similarity	NPC473238
0.7027	Intermediate Similarity	NPC472341
0.7013	Intermediate Similarity	NPC478084
0.7013	Intermediate Similarity	NPC252483
0.7013	Intermediate Similarity	NPC191345
0.7013	Intermediate Similarity	NPC31828
0.7	Intermediate Similarity	NPC11555
0.7	Intermediate Similarity	NPC60837
0.7	Intermediate Similarity	NPC2728
0.7	Intermediate Similarity	NPC208198
0.7	Intermediate Similarity	NPC227170
0.7	Intermediate Similarity	NPC282619
0.7	Intermediate Similarity	NPC172613
0.7	Intermediate Similarity	NPC470929
0.6988	Remote Similarity	NPC473436
0.6986	Remote Similarity	NPC282454
0.6974	Remote Similarity	NPC107963
0.6974	Remote Similarity	NPC470145
0.6962	Remote Similarity	NPC119922
0.6962	Remote Similarity	NPC116320
0.6957	Remote Similarity	NPC290791
0.6957	Remote Similarity	NPC292419
0.6957	Remote Similarity	NPC114891
0.6951	Remote Similarity	NPC215968
0.6951	Remote Similarity	NPC471240
0.6951	Remote Similarity	NPC155531
0.6951	Remote Similarity	NPC471410
0.6951	Remote Similarity	NPC131365
0.6951	Remote Similarity	NPC107603
0.6951	Remote Similarity	NPC471411
0.6949	Remote Similarity	NPC240994

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 NPC94897 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	533
0.1-0.2	4480
0.2-0.3	2771
0.3-0.4	902
0.4-0.5	315
0.5-0.6	128
0.6-0.7	17
0.7-0.8	3
0.8-0.85	0
0.85-0.9	1
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.873	High Similarity	NPD371	Approved
0.7571	Intermediate Similarity	NPD4267	Clinical (unspecified phase)
0.7288	Intermediate Similarity	NPD385	Approved
0.7288	Intermediate Similarity	NPD384	Approved
0.7119	Intermediate Similarity	NPD388	Approved
0.7119	Intermediate Similarity	NPD386	Approved
0.6986	Remote Similarity	NPD7532	Clinical (unspecified phase)
0.6711	Remote Similarity	NPD1811	Approved
0.6711	Remote Similarity	NPD1810	Approved
0.6623	Remote Similarity	NPD3703	Phase 2
0.6533	Remote Similarity	NPD4787	Phase 1
0.64	Remote Similarity	NPD3700	Clinical (unspecified phase)
0.64	Remote Similarity	NPD3699	Clinical (unspecified phase)
0.6375	Remote Similarity	NPD6115	Approved
0.6375	Remote Similarity	NPD6118	Approved
0.6375	Remote Similarity	NPD6114	Approved
0.6375	Remote Similarity	NPD6697	Approved
0.625	Remote Similarity	NPD6116	Phase 1
0.6234	Remote Similarity	NPD4808	Clinical (unspecified phase)
0.6234	Remote Similarity	NPD4809	Clinical (unspecified phase)
0.622	Remote Similarity	NPD6928	Phase 2
0.622	Remote Similarity	NPD7525	Registered
0.6125	Remote Similarity	NPD6117	Approved
0.6104	Remote Similarity	NPD2254	Approved
0.6104	Remote Similarity	NPD2687	Approved
0.6104	Remote Similarity	NPD2686	Approved
0.6098	Remote Similarity	NPD7645	Phase 2
0.6081	Remote Similarity	NPD3171	Clinical (unspecified phase)
0.6076	Remote Similarity	NPD6113	Clinical (unspecified phase)
0.6	Remote Similarity	NPD8996	Phase 3
0.6	Remote Similarity	NPD8995	Clinical (unspecified phase)
0.5974	Remote Similarity	NPD3698	Phase 2
0.596	Remote Similarity	NPD5345	Clinical (unspecified phase)
0.5934	Remote Similarity	NPD8171	Discontinued
0.5909	Remote Similarity	NPD7524	Approved
0.59	Remote Similarity	NPD4061	Clinical (unspecified phase)
0.5897	Remote Similarity	NPD4245	Approved
0.5897	Remote Similarity	NPD4244	Approved
0.5873	Remote Similarity	NPD9219	Approved
0.5873	Remote Similarity	NPD9218	Clinical (unspecified phase)
0.5844	Remote Similarity	NPD5360	Phase 3
0.5844	Remote Similarity	NPD5361	Clinical (unspecified phase)
0.5833	Remote Similarity	NPD6930	Phase 2
0.5833	Remote Similarity	NPD6931	Approved
0.5814	Remote Similarity	NPD3669	Approved
0.5814	Remote Similarity	NPD3670	Clinical (unspecified phase)
0.5783	Remote Similarity	NPD3671	Phase 1
0.5747	Remote Similarity	NPD7338	Clinical (unspecified phase)
0.5732	Remote Similarity	NPD3701	Clinical (unspecified phase)
0.5732	Remote Similarity	NPD6933	Approved
0.5714	Remote Similarity	NPD367	Approved
0.5714	Remote Similarity	NPD3168	Discontinued
0.5714	Remote Similarity	NPD6929	Approved
0.5696	Remote Similarity	NPD4789	Approved
0.567	Remote Similarity	NPD1700	Approved
0.567	Remote Similarity	NPD5344	Discontinued
0.567	Remote Similarity	NPD4159	Approved
0.5663	Remote Similarity	NPD6932	Approved
0.5647	Remote Similarity	NPD4748	Discontinued
0.5641	Remote Similarity	NPD6705	Phase 1
0.5632	Remote Similarity	NPD6695	Phase 3
0.5625	Remote Similarity	NPD4758	Discontinued
0.561	Remote Similarity	NPD6942	Approved
0.561	Remote Similarity	NPD7339	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