NPASS Compound

Structure

Physi-Chem Properties

Molecular Weight:	220.18
Volume:	254.401
LogP:	4.131
LogD:	3.558
LogS:	-3.737
# Rotatable Bonds:	1
TPSA:	20.23
# H-Bond Aceptor:	1
# H-Bond Donor:	1
# Rings:	2
# Heavy Atoms:	1

MedChem Properties

QED Drug-Likeness Score:	0.668
Synthetic Accessibility Score:	4.337
Fsp3:	0.733
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.395
MDCK Permeability:	1.7585873138159513e-05
Pgp-inhibitor:	0.004
Pgp-substrate:	0.001
Human Intestinal Absorption (HIA):	0.003
20% Bioavailability (F20%):	0.889
30% Bioavailability (F30%):	0.222

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.905
Plasma Protein Binding (PPB):	86.7593002319336%
Volume Distribution (VD):	1.237
Pgp-substrate:	10.046972274780273%

ADMET: Metabolism

CYP1A2-inhibitor:	0.241
CYP1A2-substrate:	0.58
CYP2C19-inhibitor:	0.107
CYP2C19-substrate:	0.922
CYP2C9-inhibitor:	0.146
CYP2C9-substrate:	0.316
CYP2D6-inhibitor:	0.051
CYP2D6-substrate:	0.678
CYP3A4-inhibitor:	0.348
CYP3A4-substrate:	0.526

ADMET: Excretion

Clearance (CL):	9.924
Half-life (T1/2):	0.09

ADMET: Toxicity

hERG Blockers:	0.009
Human Hepatotoxicity (H-HT):	0.136
Drug-inuced Liver Injury (DILI):	0.318
AMES Toxicity:	0.016
Rat Oral Acute Toxicity:	0.244
Maximum Recommended Daily Dose:	0.564
Skin Sensitization:	0.025
Carcinogencity:	0.851
Eye Corrosion:	0.003
Eye Irritation:	0.038
Respiratory Toxicity:	0.255

Download Data

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

Natural Product: NPC469320

Natural Product ID:	NPC469320
*Common Name:**	(E)-[(1S)-1-Hydroxy-1-Methyl-7-Propan-2-Yl-2,3,3A,5,6,8A-Hexahydroazulen-4-Ylidene]Methanesulfonic Acid
IUPAC Name:	(E)-[(1S)-1-hydroxy-1-methyl-7-propan-2-yl-2,3,3a,5,6,8a-hexahydroazulen-4-ylidene]methanesulfonic acid
Synonyms:
Standard InCHIKey:	DGQQFMFGQBQZSD-VWKVFTBUSA-N
Standard InCHI:	InChI=1S/C15H24O4S/c1-10(2)11-4-5-12(9-20(17,18)19)13-6-7-15(3,16)14(13)8-11/h8-10,13-14,16H,4-7H2,1-3H3,(H,17,18,19)/b12-9+/t13?,14?,15-/m0/s1
SMILES:	CC(C1=CC2C(/C(=C/S(=O)(=O)O)/CC1)CC[C@]2(C)O)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL104901
PubChem CID:	44335288
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001550] Sesquiterpenoids [CHEMONTID:0002874] Guaianes

*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
NPO30648	Alisma orientale	Species	Alismataceae	Eukaryota	rhizome	n.a.	n.a.	PMID[10560729]
NPO30648	Alisma orientale	Species	Alismataceae	Eukaryota	n.a.	rhizome	n.a.	PMID[17541191]
NPO30648	Alisma orientale	Species	Alismataceae	Eukaryota	Rhizome	n.a.	n.a.	PMID[26425784]
NPO30648	Alisma orientale	Species	Alismataceae	Eukaryota	n.a.	tuber	n.a.	PMID[26666273]
NPO30648	Alisma orientale	Species	Alismataceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]

☑ 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	5

Activity Type	# Activity
Organism	6

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT32	Organism	Mus musculus	Mus musculus	Inhibition	=	8.4	%	PMID[461220]
NPT32	Organism	Mus musculus	Mus musculus	Inhibition	=	14.3	%	PMID[461220]
NPT32	Organism	Mus musculus	Mus musculus	Inhibition	=	11.0	%	PMID[461220]
NPT32	Organism	Mus musculus	Mus musculus	Inhibition	=	21.5	%	PMID[461220]
NPT32	Organism	Mus musculus	Mus musculus	Inhibition	=	27.1	%	PMID[461220]
NPT32	Organism	Mus musculus	Mus musculus	IC50	>	100000.0	nM	PMID[461220]

☑ 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 NPC469320 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	160
0.1-0.2	2584
0.2-0.3	18548
0.3-0.4	12387
0.4-0.5	7511
0.5-0.6	1405
0.6-0.7	83
0.7-0.8	16
0.8-0.85	1
0.85-0.9	0
0.9-0.95	1
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
0.9306	High Similarity	NPC469324
0.8209	Intermediate Similarity	NPC469321
0.7887	Intermediate Similarity	NPC205618
0.7887	Intermediate Similarity	NPC261782
0.7887	Intermediate Similarity	NPC469326
0.7647	Intermediate Similarity	NPC278550
0.7467	Intermediate Similarity	NPC144647
0.7465	Intermediate Similarity	NPC63111
0.7368	Intermediate Similarity	NPC471781
0.7324	Intermediate Similarity	NPC252809
0.7123	Intermediate Similarity	NPC474480
0.7105	Intermediate Similarity	NPC224532
0.7051	Intermediate Similarity	NPC41886
0.6974	Remote Similarity	NPC136813
0.6962	Remote Similarity	NPC300940
0.6944	Remote Similarity	NPC310228
0.6944	Remote Similarity	NPC5698
0.6944	Remote Similarity	NPC52431
0.6849	Remote Similarity	NPC323153
0.6835	Remote Similarity	NPC471660
0.6812	Remote Similarity	NPC192962
0.679	Remote Similarity	NPC77501
0.6761	Remote Similarity	NPC274396
0.6757	Remote Similarity	NPC274704
0.6753	Remote Similarity	NPC472255
0.6753	Remote Similarity	NPC472253
0.6712	Remote Similarity	NPC99480
0.6712	Remote Similarity	NPC184049
0.6711	Remote Similarity	NPC238352
0.6711	Remote Similarity	NPC477009
0.6707	Remote Similarity	NPC126969
0.6667	Remote Similarity	NPC471659
0.6667	Remote Similarity	NPC279200
0.6667	Remote Similarity	NPC167527
0.6625	Remote Similarity	NPC469737
0.6623	Remote Similarity	NPC272125
0.6622	Remote Similarity	NPC135648
0.6588	Remote Similarity	NPC30675
0.6575	Remote Similarity	NPC475830
0.6533	Remote Similarity	NPC210346
0.6506	Remote Similarity	NPC471658
0.65	Remote Similarity	NPC470041
0.6471	Remote Similarity	NPC84185
0.6471	Remote Similarity	NPC471890
0.6471	Remote Similarity	NPC66677
0.6463	Remote Similarity	NPC309178
0.6447	Remote Similarity	NPC211291
0.6447	Remote Similarity	NPC133368
0.6429	Remote Similarity	NPC306195
0.6429	Remote Similarity	NPC35519
0.6429	Remote Similarity	NPC179169
0.6429	Remote Similarity	NPC181255
0.6429	Remote Similarity	NPC157781
0.641	Remote Similarity	NPC469328
0.6395	Remote Similarity	NPC164218
0.6389	Remote Similarity	NPC218525
0.6386	Remote Similarity	NPC265921
0.6386	Remote Similarity	NPC215215
0.6386	Remote Similarity	NPC251435
0.6386	Remote Similarity	NPC85831
0.6377	Remote Similarity	NPC329773
0.6375	Remote Similarity	NPC474900
0.6341	Remote Similarity	NPC234527
0.6341	Remote Similarity	NPC14352
0.6329	Remote Similarity	NPC477791
0.6316	Remote Similarity	NPC15152
0.631	Remote Similarity	NPC310643
0.631	Remote Similarity	NPC476317
0.631	Remote Similarity	NPC215481
0.6286	Remote Similarity	NPC214584
0.6286	Remote Similarity	NPC26906
0.6282	Remote Similarity	NPC187619
0.6265	Remote Similarity	NPC329090
0.6265	Remote Similarity	NPC27395
0.625	Remote Similarity	NPC133844
0.625	Remote Similarity	NPC472465
0.6222	Remote Similarity	NPC146850
0.6222	Remote Similarity	NPC287015
0.622	Remote Similarity	NPC471662
0.6207	Remote Similarity	NPC471656
0.6203	Remote Similarity	NPC230107
0.6197	Remote Similarity	NPC177112
0.6197	Remote Similarity	NPC71506
0.619	Remote Similarity	NPC319090
0.619	Remote Similarity	NPC328104
0.619	Remote Similarity	NPC113639
0.619	Remote Similarity	NPC313185
0.6184	Remote Similarity	NPC162109
0.618	Remote Similarity	NPC471340
0.6163	Remote Similarity	NPC470944
0.6163	Remote Similarity	NPC477522
0.6154	Remote Similarity	NPC309300
0.6136	Remote Similarity	NPC471661
0.6118	Remote Similarity	NPC96319
0.6118	Remote Similarity	NPC152017
0.6118	Remote Similarity	NPC315261
0.6111	Remote Similarity	NPC90446
0.6098	Remote Similarity	NPC475728
0.6067	Remote Similarity	NPC470614
0.6067	Remote Similarity	NPC1272
0.6053	Remote Similarity	NPC122239
0.6047	Remote Similarity	NPC318495
0.6047	Remote Similarity	NPC471454
0.6047	Remote Similarity	NPC198968
0.6047	Remote Similarity	NPC276769
0.6047	Remote Similarity	NPC155986
0.6044	Remote Similarity	NPC471185
0.6026	Remote Similarity	NPC473508
0.6024	Remote Similarity	NPC106309
0.6023	Remote Similarity	NPC26117
0.6	Remote Similarity	NPC476924
0.6	Remote Similarity	NPC60818
0.6	Remote Similarity	NPC23231
0.6	Remote Similarity	NPC267027
0.6	Remote Similarity	NPC162309
0.6	Remote Similarity	NPC197089
0.5978	Remote Similarity	NPC477604
0.5978	Remote Similarity	NPC152808
0.5978	Remote Similarity	NPC293287
0.5977	Remote Similarity	NPC477514
0.5977	Remote Similarity	NPC475337
0.5976	Remote Similarity	NPC22301
0.5976	Remote Similarity	NPC167272
0.5976	Remote Similarity	NPC217570
0.5976	Remote Similarity	NPC90115
0.5976	Remote Similarity	NPC269877
0.5974	Remote Similarity	NPC240506
0.5974	Remote Similarity	NPC99487
0.5974	Remote Similarity	NPC66020
0.5955	Remote Similarity	NPC320525
0.5955	Remote Similarity	NPC78677
0.5955	Remote Similarity	NPC59994
0.5952	Remote Similarity	NPC474140
0.5949	Remote Similarity	NPC287744
0.5949	Remote Similarity	NPC300593
0.5949	Remote Similarity	NPC140233
0.5949	Remote Similarity	NPC219940
0.5934	Remote Similarity	NPC116613
0.5934	Remote Similarity	NPC478102
0.5934	Remote Similarity	NPC124172
0.593	Remote Similarity	NPC107059
0.593	Remote Similarity	NPC473437
0.593	Remote Similarity	NPC124289
0.593	Remote Similarity	NPC141346
0.593	Remote Similarity	NPC142759
0.593	Remote Similarity	NPC115719
0.593	Remote Similarity	NPC321381
0.593	Remote Similarity	NPC321016
0.593	Remote Similarity	NPC25908
0.5926	Remote Similarity	NPC163290
0.5921	Remote Similarity	NPC10017
0.5921	Remote Similarity	NPC155025
0.5914	Remote Similarity	NPC191283
0.5914	Remote Similarity	NPC475313
0.5909	Remote Similarity	NPC181195
0.5909	Remote Similarity	NPC1319
0.5909	Remote Similarity	NPC261125
0.5909	Remote Similarity	NPC328714
0.5904	Remote Similarity	NPC254845
0.5904	Remote Similarity	NPC133873
0.5904	Remote Similarity	NPC49422
0.5904	Remote Similarity	NPC9161
0.5897	Remote Similarity	NPC79576
0.5897	Remote Similarity	NPC194208
0.5897	Remote Similarity	NPC282694
0.5895	Remote Similarity	NPC470832
0.5895	Remote Similarity	NPC301969
0.5895	Remote Similarity	NPC37607
0.5889	Remote Similarity	NPC201852
0.5889	Remote Similarity	NPC193347
0.5882	Remote Similarity	NPC7382
0.5882	Remote Similarity	NPC206875
0.5875	Remote Similarity	NPC19569
0.5875	Remote Similarity	NPC471200
0.587	Remote Similarity	NPC474189
0.587	Remote Similarity	NPC318390
0.587	Remote Similarity	NPC474349
0.5862	Remote Similarity	NPC472014
0.5862	Remote Similarity	NPC476439
0.5854	Remote Similarity	NPC160209
0.5844	Remote Similarity	NPC475931
0.5843	Remote Similarity	NPC236237
0.5843	Remote Similarity	NPC102253
0.5843	Remote Similarity	NPC322313
0.5843	Remote Similarity	NPC186072
0.5843	Remote Similarity	NPC209944
0.5843	Remote Similarity	NPC241290
0.5843	Remote Similarity	NPC324772
0.5843	Remote Similarity	NPC164840
0.5833	Remote Similarity	NPC477792
0.5833	Remote Similarity	NPC94127
0.5824	Remote Similarity	NPC477667
0.5824	Remote Similarity	NPC320548
0.5824	Remote Similarity	NPC472473
0.5824	Remote Similarity	NPC477852
0.5824	Remote Similarity	NPC474634
0.5824	Remote Similarity	NPC110778
0.5823	Remote Similarity	NPC174956
0.5821	Remote Similarity	NPC473912
0.5816	Remote Similarity	NPC67584

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 NPC469320 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	151
0.1-0.2	2770
0.2-0.3	4549
0.3-0.4	1248
0.4-0.5	315
0.5-0.6	109
0.6-0.7	8
0.7-0.8	0
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
0.6463	Remote Similarity	NPD4785	Approved
0.6463	Remote Similarity	NPD4784	Approved
0.642	Remote Similarity	NPD4243	Approved
0.6265	Remote Similarity	NPD6924	Approved
0.6265	Remote Similarity	NPD6926	Approved
0.6237	Remote Similarity	NPD7136	Phase 2
0.619	Remote Similarity	NPD4190	Phase 3
0.619	Remote Similarity	NPD5275	Approved
0.6118	Remote Similarity	NPD3701	Clinical (unspecified phase)
0.6118	Remote Similarity	NPD6933	Approved
0.6092	Remote Similarity	NPD4195	Approved
0.6023	Remote Similarity	NPD4819	Approved
0.6023	Remote Similarity	NPD4821	Approved
0.6023	Remote Similarity	NPD4820	Approved
0.6023	Remote Similarity	NPD4822	Approved
0.6	Remote Similarity	NPD5332	Approved
0.6	Remote Similarity	NPD5362	Discontinued
0.6	Remote Similarity	NPD5331	Approved
0.5976	Remote Similarity	NPD6922	Approved
0.5976	Remote Similarity	NPD6923	Approved
0.5955	Remote Similarity	NPD5369	Approved
0.5955	Remote Similarity	NPD4790	Discontinued
0.5904	Remote Similarity	NPD7143	Approved
0.5904	Remote Similarity	NPD7144	Approved
0.5889	Remote Similarity	NPD4221	Approved
0.5889	Remote Similarity	NPD4223	Phase 3
0.5862	Remote Similarity	NPD6932	Approved
0.5843	Remote Similarity	NPD6931	Approved
0.5843	Remote Similarity	NPD6930	Phase 2
0.5843	Remote Similarity	NPD7525	Registered
0.5833	Remote Similarity	NPD7151	Approved
0.5833	Remote Similarity	NPD7152	Approved
0.5833	Remote Similarity	NPD7150	Approved
0.5824	Remote Similarity	NPD6695	Phase 3
0.5814	Remote Similarity	NPD7339	Approved
0.5814	Remote Similarity	NPD6942	Approved
0.5795	Remote Similarity	NPD4268	Approved
0.5795	Remote Similarity	NPD4271	Approved
0.5761	Remote Similarity	NPD3668	Phase 3
0.5761	Remote Similarity	NPD7338	Clinical (unspecified phase)
0.5761	Remote Similarity	NPD4197	Approved
0.5745	Remote Similarity	NPD4751	Clinical (unspecified phase)
0.573	Remote Similarity	NPD6683	Phase 2
0.573	Remote Similarity	NPD6929	Approved
0.5728	Remote Similarity	NPD4754	Approved
0.5714	Remote Similarity	NPD4269	Approved
0.5714	Remote Similarity	NPD4270	Approved
0.5699	Remote Similarity	NPD6082	Clinical (unspecified phase)
0.5699	Remote Similarity	NPD5329	Approved
0.5696	Remote Similarity	NPD368	Approved
0.5684	Remote Similarity	NPD4518	Approved
0.5682	Remote Similarity	NPD5776	Phase 2
0.5682	Remote Similarity	NPD6925	Approved
0.5667	Remote Similarity	NPD5790	Clinical (unspecified phase)
0.5667	Remote Similarity	NPD7509	Discontinued
0.5667	Remote Similarity	NPD7514	Phase 3
0.5667	Remote Similarity	NPD4748	Discontinued
0.5667	Remote Similarity	NPD5368	Approved
0.5638	Remote Similarity	NPD4688	Approved
0.5638	Remote Similarity	NPD4693	Phase 3
0.5638	Remote Similarity	NPD5205	Approved
0.5638	Remote Similarity	NPD4689	Approved
0.5638	Remote Similarity	NPD4138	Approved
0.5638	Remote Similarity	NPD5690	Phase 2
0.5638	Remote Similarity	NPD4690	Approved
0.5638	Remote Similarity	NPD4694	Approved
0.5638	Remote Similarity	NPD5280	Approved
0.5625	Remote Similarity	NPD4753	Phase 2
0.5618	Remote Similarity	NPD7322	Clinical (unspecified phase)
0.5618	Remote Similarity	NPD7145	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