NPASS Compound

Structure

Physi-Chem Properties

Molecular Weight:	440.2
Volume:	443.805
LogP:	1.458
LogD:	0.879
LogS:	-1.755
# Rotatable Bonds:	10
TPSA:	139.59
# H-Bond Aceptor:	9
# H-Bond Donor:	3
# Rings:	1
# Heavy Atoms:	9

MedChem Properties

QED Drug-Likeness Score:	0.302
Synthetic Accessibility Score:	4.56
Fsp3:	0.591
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
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:	-4.762
MDCK Permeability:	5.595169204752892e-05
Pgp-inhibitor:	0.997
Pgp-substrate:	0.495
Human Intestinal Absorption (HIA):	0.949
20% Bioavailability (F20%):	0.653
30% Bioavailability (F30%):	0.993

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.098
Plasma Protein Binding (PPB):	77.2498550415039%
Volume Distribution (VD):	1.331
Pgp-substrate:	9.532824516296387%

ADMET: Metabolism

CYP1A2-inhibitor:	0.343
CYP1A2-substrate:	0.515
CYP2C19-inhibitor:	0.419
CYP2C19-substrate:	0.672
CYP2C9-inhibitor:	0.902
CYP2C9-substrate:	0.317
CYP2D6-inhibitor:	0.557
CYP2D6-substrate:	0.053
CYP3A4-inhibitor:	0.821
CYP3A4-substrate:	0.149

ADMET: Excretion

Clearance (CL):	3.037
Half-life (T1/2):	0.942

ADMET: Toxicity

hERG Blockers:	0.028
Human Hepatotoxicity (H-HT):	0.934
Drug-inuced Liver Injury (DILI):	0.303
AMES Toxicity:	0.007
Rat Oral Acute Toxicity:	0.016
Maximum Recommended Daily Dose:	0.087
Skin Sensitization:	0.914
Carcinogencity:	0.018
Eye Corrosion:	0.022
Eye Irritation:	0.057
Respiratory Toxicity:	0.081

Download Data

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

Natural Product: NPC477314

Natural Product ID:	NPC477314
*Common Name:**	[(1S,2R,3R,4S,5R,6S)-2,3,6-trihydroxy-4,5-bis[[(Z)-2-methylbut-2-enoyl]oxy]cyclohexyl] (E)-3-methylpent-2-enoate
IUPAC Name:	[(1S,2R,3R,4S,5R,6S)-2,3,6-trihydroxy-4,5-bis[[(Z)-2-methylbut-2-enoyl]oxy]cyclohexyl] (E)-3-methylpent-2-enoate
Synonyms:
Standard InCHIKey:	BVHSIMOPFXDATD-JFNFRUKESA-N
Standard InCHI:	InChI=1S/C22H32O9/c1-7-11(4)10-14(23)29-18-15(24)16(25)19(30-21(27)12(5)8-2)20(17(18)26)31-22(28)13(6)9-3/h8-10,15-20,24-26H,7H2,1-6H3/b11-10+,12-8-,13-9-/t15-,16-,17+,18+,19+,20-/m1/s1
SMILES:	CC/C(=C/C(=O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H]([C@H]1O)OC(=O)/C(=C\C)/C)OC(=O)/C(=C\C)/C)O)O)/C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	122195886
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000264] Organic acids and derivatives [CHEMONTID:0000265] Carboxylic acids and derivatives [CHEMONTID:0001986] Tricarboxylic acids and derivatives

*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
NPO30455	Inula cappa	Species	Asteraceae	Eukaryota	Whole Plant	Yulin County, Guangxi Province, China	2012-SEP	PMID[26444098]

☑ 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

Activity Type	# Activity
Cell Line	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT113	Cell Line	RAW264.7	Mus musculus	IC50	=	8400	nM	PMID[26444098]

☑ 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 NPC477314 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	159
0.1-0.2	2122
0.2-0.3	6128
0.3-0.4	15532
0.4-0.5	11243
0.5-0.6	5824
0.6-0.7	1485
0.7-0.8	175
0.8-0.85	10
0.85-0.9	7
0.9-0.95	11
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
0.9444	High Similarity	NPC477315
0.9444	High Similarity	NPC477304
0.9444	High Similarity	NPC477309
0.9444	High Similarity	NPC477312
0.9444	High Similarity	NPC477305
0.9444	High Similarity	NPC477313
0.9444	High Similarity	NPC477316
0.9444	High Similarity	NPC477308
0.9315	High Similarity	NPC477306
0.9306	High Similarity	NPC477311
0.9306	High Similarity	NPC477303
0.8125	Intermediate Similarity	NPC180725
0.8101	Intermediate Similarity	NPC474026
0.8101	Intermediate Similarity	NPC475711
0.809	Intermediate Similarity	NPC472995
0.8025	Intermediate Similarity	NPC133226
0.8025	Intermediate Similarity	NPC470147
0.8	Intermediate Similarity	NPC248775
0.8	Intermediate Similarity	NPC475186
0.8	Intermediate Similarity	NPC118077
0.7976	Intermediate Similarity	NPC470124
0.7927	Intermediate Similarity	NPC469469
0.7901	Intermediate Similarity	NPC470149
0.7901	Intermediate Similarity	NPC470148
0.7857	Intermediate Similarity	NPC475035
0.7857	Intermediate Similarity	NPC266718
0.7831	Intermediate Similarity	NPC251026
0.7816	Intermediate Similarity	NPC285588
0.7805	Intermediate Similarity	NPC127295
0.7805	Intermediate Similarity	NPC163362
0.7791	Intermediate Similarity	NPC475037
0.7778	Intermediate Similarity	NPC469583
0.7765	Intermediate Similarity	NPC477013
0.7765	Intermediate Similarity	NPC329615
0.7765	Intermediate Similarity	NPC477014
0.7765	Intermediate Similarity	NPC471567
0.7765	Intermediate Similarity	NPC475034
0.7765	Intermediate Similarity	NPC329838
0.7765	Intermediate Similarity	NPC120398
0.7738	Intermediate Similarity	NPC142111
0.7738	Intermediate Similarity	NPC473315
0.7701	Intermediate Similarity	NPC473905
0.7701	Intermediate Similarity	NPC48338
0.7701	Intermediate Similarity	NPC280621
0.7701	Intermediate Similarity	NPC20339
0.7701	Intermediate Similarity	NPC40376
0.7701	Intermediate Similarity	NPC320458
0.7701	Intermediate Similarity	NPC89001
0.7701	Intermediate Similarity	NPC21208
0.7701	Intermediate Similarity	NPC233551
0.7692	Intermediate Similarity	NPC472997
0.7692	Intermediate Similarity	NPC472996
0.7674	Intermediate Similarity	NPC477015
0.7674	Intermediate Similarity	NPC47937
0.7647	Intermediate Similarity	NPC163093
0.7647	Intermediate Similarity	NPC473308
0.7647	Intermediate Similarity	NPC156804
0.764	Intermediate Similarity	NPC110072
0.7625	Intermediate Similarity	NPC285840
0.7625	Intermediate Similarity	NPC327041
0.7614	Intermediate Similarity	NPC477016
0.7614	Intermediate Similarity	NPC477017
0.7609	Intermediate Similarity	NPC472998
0.7595	Intermediate Similarity	NPC327383
0.7595	Intermediate Similarity	NPC185186
0.7586	Intermediate Similarity	NPC258068
0.7586	Intermediate Similarity	NPC476583
0.7586	Intermediate Similarity	NPC178215
0.7586	Intermediate Similarity	NPC20533
0.7564	Intermediate Similarity	NPC476012
0.7561	Intermediate Similarity	NPC317263
0.7558	Intermediate Similarity	NPC182383
0.7558	Intermediate Similarity	NPC322529
0.7556	Intermediate Similarity	NPC238090
0.7556	Intermediate Similarity	NPC472196
0.7556	Intermediate Similarity	NPC472195
0.7528	Intermediate Similarity	NPC177668
0.7528	Intermediate Similarity	NPC239517
0.7528	Intermediate Similarity	NPC118078
0.75	Intermediate Similarity	NPC107654
0.75	Intermediate Similarity	NPC470137
0.7473	Intermediate Similarity	NPC159698
0.7471	Intermediate Similarity	NPC240695
0.7471	Intermediate Similarity	NPC219652
0.7471	Intermediate Similarity	NPC241360
0.7471	Intermediate Similarity	NPC62118
0.7471	Intermediate Similarity	NPC107717
0.7471	Intermediate Similarity	NPC114694
0.7471	Intermediate Similarity	NPC103523
0.7471	Intermediate Similarity	NPC25703
0.7471	Intermediate Similarity	NPC473840
0.7471	Intermediate Similarity	NPC293136
0.7471	Intermediate Similarity	NPC134865
0.7471	Intermediate Similarity	NPC231096
0.7471	Intermediate Similarity	NPC132940
0.7471	Intermediate Similarity	NPC208473
0.7471	Intermediate Similarity	NPC282815
0.7471	Intermediate Similarity	NPC171174
0.7471	Intermediate Similarity	NPC232555
0.7471	Intermediate Similarity	NPC142117
0.7471	Intermediate Similarity	NPC475581
0.747	Intermediate Similarity	NPC1180
0.7468	Intermediate Similarity	NPC475762
0.7444	Intermediate Similarity	NPC477749
0.7439	Intermediate Similarity	NPC477203
0.7416	Intermediate Similarity	NPC473504
0.7416	Intermediate Similarity	NPC42598
0.7416	Intermediate Similarity	NPC133450
0.7416	Intermediate Similarity	NPC40066
0.7416	Intermediate Similarity	NPC91067
0.7416	Intermediate Similarity	NPC81778
0.7416	Intermediate Similarity	NPC477011
0.7416	Intermediate Similarity	NPC20621
0.7416	Intermediate Similarity	NPC93794
0.7416	Intermediate Similarity	NPC318963
0.7416	Intermediate Similarity	NPC280612
0.7412	Intermediate Similarity	NPC131002
0.7412	Intermediate Similarity	NPC473529
0.7412	Intermediate Similarity	NPC94875
0.7412	Intermediate Similarity	NPC475159
0.7412	Intermediate Similarity	NPC180363
0.7412	Intermediate Similarity	NPC65930
0.7412	Intermediate Similarity	NPC329829
0.7412	Intermediate Similarity	NPC473712
0.7412	Intermediate Similarity	NPC73310
0.7412	Intermediate Similarity	NPC145914
0.7412	Intermediate Similarity	NPC473780
0.7412	Intermediate Similarity	NPC11332
0.7386	Intermediate Similarity	NPC473995
0.7375	Intermediate Similarity	NPC329914
0.7368	Intermediate Similarity	NPC19769
0.7356	Intermediate Similarity	NPC473669
0.7356	Intermediate Similarity	NPC470400
0.7356	Intermediate Similarity	NPC283085
0.7356	Intermediate Similarity	NPC235809
0.7356	Intermediate Similarity	NPC1083
0.7356	Intermediate Similarity	NPC103284
0.7356	Intermediate Similarity	NPC110710
0.7356	Intermediate Similarity	NPC66346
0.7356	Intermediate Similarity	NPC473156
0.7356	Intermediate Similarity	NPC231009
0.7356	Intermediate Similarity	NPC319036
0.7356	Intermediate Similarity	NPC25764
0.7356	Intermediate Similarity	NPC477018
0.7356	Intermediate Similarity	NPC77871
0.7356	Intermediate Similarity	NPC39167
0.7356	Intermediate Similarity	NPC39279
0.7356	Intermediate Similarity	NPC132496
0.7356	Intermediate Similarity	NPC9678
0.7356	Intermediate Similarity	NPC473651
0.7356	Intermediate Similarity	NPC473671
0.7356	Intermediate Similarity	NPC223871
0.7356	Intermediate Similarity	NPC292809
0.7356	Intermediate Similarity	NPC100921
0.7356	Intermediate Similarity	NPC475268
0.7356	Intermediate Similarity	NPC286338
0.7356	Intermediate Similarity	NPC107986
0.7356	Intermediate Similarity	NPC82795
0.7356	Intermediate Similarity	NPC202055
0.7356	Intermediate Similarity	NPC473478
0.7342	Intermediate Similarity	NPC476037
0.7342	Intermediate Similarity	NPC202011
0.7333	Intermediate Similarity	NPC473311
0.7333	Intermediate Similarity	NPC3952
0.7333	Intermediate Similarity	NPC6414
0.7333	Intermediate Similarity	NPC473904
0.7333	Intermediate Similarity	NPC303451
0.7326	Intermediate Similarity	NPC144415
0.7326	Intermediate Similarity	NPC253801
0.7317	Intermediate Similarity	NPC477202
0.7317	Intermediate Similarity	NPC469880
0.7317	Intermediate Similarity	NPC326661
0.7303	Intermediate Similarity	NPC274446
0.7303	Intermediate Similarity	NPC172821
0.7303	Intermediate Similarity	NPC287164
0.7303	Intermediate Similarity	NPC133730
0.7303	Intermediate Similarity	NPC39754
0.7303	Intermediate Similarity	NPC100454
0.7303	Intermediate Similarity	NPC242364
0.7303	Intermediate Similarity	NPC234077
0.7303	Intermediate Similarity	NPC81045
0.7303	Intermediate Similarity	NPC151403
0.7303	Intermediate Similarity	NPC61257
0.7303	Intermediate Similarity	NPC171135
0.7303	Intermediate Similarity	NPC261952
0.7303	Intermediate Similarity	NPC169511
0.7303	Intermediate Similarity	NPC320569
0.7303	Intermediate Similarity	NPC191929
0.7284	Intermediate Similarity	NPC315843
0.7283	Intermediate Similarity	NPC256368
0.7283	Intermediate Similarity	NPC294293
0.7273	Intermediate Similarity	NPC276299
0.7273	Intermediate Similarity	NPC477010
0.7273	Intermediate Similarity	NPC279267
0.7273	Intermediate Similarity	NPC308412
0.7273	Intermediate Similarity	NPC201356
0.7273	Intermediate Similarity	NPC473687
0.7273	Intermediate Similarity	NPC69082
0.7273	Intermediate Similarity	NPC210218
0.7273	Intermediate Similarity	NPC204686

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 NPC477314 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	146
0.1-0.2	2497
0.2-0.3	4012
0.3-0.4	1808
0.4-0.5	537
0.5-0.6	139
0.6-0.7	8
0.7-0.8	3
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
0.7528	Intermediate Similarity	NPD46	Approved
0.7528	Intermediate Similarity	NPD7838	Discovery
0.7528	Intermediate Similarity	NPD6698	Approved
0.7368	Intermediate Similarity	NPD5344	Discontinued
0.6907	Remote Similarity	NPD6648	Approved
0.6804	Remote Similarity	NPD8029	Clinical (unspecified phase)
0.6765	Remote Similarity	NPD6686	Approved
0.6556	Remote Similarity	NPD6110	Phase 1
0.6526	Remote Similarity	NPD7983	Approved
0.6346	Remote Similarity	NPD7899	Clinical (unspecified phase)
0.6306	Remote Similarity	NPD7516	Approved
0.63	Remote Similarity	NPD4225	Approved
0.6226	Remote Similarity	NPD4061	Clinical (unspecified phase)
0.6216	Remote Similarity	NPD7327	Approved
0.6216	Remote Similarity	NPD7328	Approved
0.6168	Remote Similarity	NPD6371	Approved
0.6154	Remote Similarity	NPD6109	Phase 1
0.6145	Remote Similarity	NPD4247	Clinical (unspecified phase)
0.6139	Remote Similarity	NPD7638	Approved
0.6129	Remote Similarity	NPD6400	Clinical (unspecified phase)
0.6098	Remote Similarity	NPD2685	Clinical (unspecified phase)
0.6081	Remote Similarity	NPD6927	Phase 3
0.6078	Remote Similarity	NPD7639	Approved
0.6078	Remote Similarity	NPD7640	Approved
0.602	Remote Similarity	NPD7637	Suspended
0.6019	Remote Similarity	NPD5955	Clinical (unspecified phase)
0.6	Remote Similarity	NPD4246	Clinical (unspecified phase)
0.5963	Remote Similarity	NPD8413	Clinical (unspecified phase)
0.5949	Remote Similarity	NPD69	Approved
0.5949	Remote Similarity	NPD9119	Approved
0.5938	Remote Similarity	NPD4251	Approved
0.5938	Remote Similarity	NPD4250	Approved
0.593	Remote Similarity	NPD7532	Clinical (unspecified phase)
0.5913	Remote Similarity	NPD7503	Approved
0.5913	Remote Similarity	NPD8380	Approved
0.5913	Remote Similarity	NPD8378	Approved
0.5913	Remote Similarity	NPD8335	Approved
0.5913	Remote Similarity	NPD8296	Approved
0.5913	Remote Similarity	NPD8379	Approved
0.5895	Remote Similarity	NPD6082	Clinical (unspecified phase)
0.587	Remote Similarity	NPD5790	Clinical (unspecified phase)
0.5833	Remote Similarity	NPD4249	Approved
0.5826	Remote Similarity	NPD8377	Approved
0.5826	Remote Similarity	NPD8294	Approved
0.5823	Remote Similarity	NPD9118	Approved
0.5783	Remote Similarity	NPD3197	Phase 1
0.5776	Remote Similarity	NPD8033	Approved
0.5773	Remote Similarity	NPD7524	Approved
0.575	Remote Similarity	NPD585	Clinical (unspecified phase)
0.5741	Remote Similarity	NPD5954	Clinical (unspecified phase)
0.5729	Remote Similarity	NPD1733	Clinical (unspecified phase)
0.5727	Remote Similarity	NPD6421	Discontinued
0.5714	Remote Similarity	NPD4756	Discovery
0.5714	Remote Similarity	NPD7507	Approved
0.5702	Remote Similarity	NPD7319	Approved
0.5694	Remote Similarity	NPD9218	Clinical (unspecified phase)
0.5694	Remote Similarity	NPD9219	Approved
0.5688	Remote Similarity	NPD5345	Clinical (unspecified phase)
0.5684	Remote Similarity	NPD7154	Phase 3
0.5678	Remote Similarity	NPD7829	Approved
0.5678	Remote Similarity	NPD7830	Approved
0.5652	Remote Similarity	NPD4268	Approved
0.5652	Remote Similarity	NPD4271	Approved
0.5644	Remote Similarity	NPD5779	Approved
0.5644	Remote Similarity	NPD5778	Approved
0.5631	Remote Similarity	NPD4792	Clinical (unspecified phase)
0.5631	Remote Similarity	NPD7839	Suspended
0.5625	Remote Similarity	NPD6053	Discontinued
0.56	Remote Similarity	NPD8522	Clinical (unspecified phase)
0.56	Remote Similarity	NPD5785	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