NPASS Compound

Structure

Physi-Chem Properties

Molecular Weight:	184.11
Volume:	182.218
LogP:	1.455
LogD:	1.925
LogS:	-0.837
# Rotatable Bonds:	0
TPSA:	38.69
# H-Bond Aceptor:	3
# H-Bond Donor:	1
# Rings:	4
# Heavy Atoms:	3

MedChem Properties

QED Drug-Likeness Score:	0.604
Synthetic Accessibility Score:	5.957
Fsp3:	1.0
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.705
MDCK Permeability:	3.772101626964286e-05
Pgp-inhibitor:	0.04
Pgp-substrate:	0.36
Human Intestinal Absorption (HIA):	0.005
20% Bioavailability (F20%):	0.004
30% Bioavailability (F30%):	0.103

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.763
Plasma Protein Binding (PPB):	12.170600891113281%
Volume Distribution (VD):	1.377
Pgp-substrate:	76.23821258544922%

ADMET: Metabolism

CYP1A2-inhibitor:	0.026
CYP1A2-substrate:	0.952
CYP2C19-inhibitor:	0.018
CYP2C19-substrate:	0.802
CYP2C9-inhibitor:	0.005
CYP2C9-substrate:	0.042
CYP2D6-inhibitor:	0.006
CYP2D6-substrate:	0.198
CYP3A4-inhibitor:	0.008
CYP3A4-substrate:	0.25

ADMET: Excretion

Clearance (CL):	15.505
Half-life (T1/2):	0.484

ADMET: Toxicity

hERG Blockers:	0.043
Human Hepatotoxicity (H-HT):	0.282
Drug-inuced Liver Injury (DILI):	0.161
AMES Toxicity:	0.062
Rat Oral Acute Toxicity:	0.573
Maximum Recommended Daily Dose:	0.107
Skin Sensitization:	0.554
Carcinogencity:	0.904
Eye Corrosion:	0.962
Eye Irritation:	0.979
Respiratory Toxicity:	0.977

Download Data

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

Natural Product: NPC470659

Natural Product ID:	NPC470659
*Common Name:**	BYWPUNIXQZJWRS-RSMBCMNPSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	BYWPUNIXQZJWRS-RSMBCMNPSA-N
Standard InCHI:	InChI=1S/C10H16O3/c1-5-6-3-8(11)10(2)7(6)4-12-9(5)13-10/h5-9,11H,3-4H2,1-2H3/t5-,6+,7+,8-,9-,10-/m0/s1
SMILES:	C[C@@H]1[C@H]2OC[C@@H]3[C@@H]1C[C@@H]([C@]3(O2)C)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL2152452
PubChem CID:	71449448
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0001729] Oxepanes

*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
NPO14197	Patrinia scabra	Species	Caprifoliaceae	Eukaryota	Roots	n.a.	n.a.	PMID[23002924]
NPO14197	Patrinia scabra	Species	Caprifoliaceae	Eukaryota	Roots	n.a.	n.a.	PMID[29799195]
NPO14197	Patrinia scabra	Species	Caprifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO14197	Patrinia scabra	Species	Caprifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO14197	Patrinia scabra	Species	Caprifoliaceae	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	2

Activity Type	# Activity
Cell Line	1
NON-MOLECULAR	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT165	Cell Line	HeLa	Homo sapiens	IC50	>	50000.0	nM	PMID[559983]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	IC50	>	50000.0	nM	PMID[559983]

☑ 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 NPC470659 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	406
0.1-0.2	4525
0.2-0.3	14920
0.3-0.4	10401
0.4-0.5	6406
0.5-0.6	4069
0.6-0.7	1589
0.7-0.8	367
0.8-0.85	11
0.85-0.9	0
0.9-0.95	1
0.95-1	2

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC470660
0.9571	High Similarity	NPC279575
0.9178	High Similarity	NPC170595
0.8873	High Similarity	NPC248427
0.8272	Intermediate Similarity	NPC31349
0.8158	Intermediate Similarity	NPC188793
0.8148	Intermediate Similarity	NPC470657
0.8125	Intermediate Similarity	NPC474156
0.7917	Intermediate Similarity	NPC477760
0.7917	Intermediate Similarity	NPC477759
0.7917	Intermediate Similarity	NPC477758
0.7917	Intermediate Similarity	NPC477754
0.7917	Intermediate Similarity	NPC477761
0.7831	Intermediate Similarity	NPC472396
0.7778	Intermediate Similarity	NPC477751
0.7778	Intermediate Similarity	NPC477752
0.7778	Intermediate Similarity	NPC477764
0.7778	Intermediate Similarity	NPC477756
0.7763	Intermediate Similarity	NPC166250
0.775	Intermediate Similarity	NPC216941
0.7701	Intermediate Similarity	NPC309866
0.7674	Intermediate Similarity	NPC36372
0.7654	Intermediate Similarity	NPC475849
0.7647	Intermediate Similarity	NPC102725
0.7614	Intermediate Similarity	NPC474399
0.7614	Intermediate Similarity	NPC92196
0.759	Intermediate Similarity	NPC290612
0.7586	Intermediate Similarity	NPC277774
0.7561	Intermediate Similarity	NPC474266
0.7558	Intermediate Similarity	NPC65550
0.7558	Intermediate Similarity	NPC279329
0.7558	Intermediate Similarity	NPC223143
0.7532	Intermediate Similarity	NPC308489
0.7532	Intermediate Similarity	NPC138273
0.7529	Intermediate Similarity	NPC281004
0.7529	Intermediate Similarity	NPC148534
0.75	Intermediate Similarity	NPC171484
0.75	Intermediate Similarity	NPC252253
0.75	Intermediate Similarity	NPC45959
0.75	Intermediate Similarity	NPC149018
0.7471	Intermediate Similarity	NPC473830
0.7471	Intermediate Similarity	NPC204881
0.7471	Intermediate Similarity	NPC293609
0.7471	Intermediate Similarity	NPC59006
0.7471	Intermediate Similarity	NPC235051
0.747	Intermediate Similarity	NPC98276
0.747	Intermediate Similarity	NPC259296
0.7468	Intermediate Similarity	NPC70996
0.7468	Intermediate Similarity	NPC214030
0.7468	Intermediate Similarity	NPC83108
0.7444	Intermediate Similarity	NPC274200
0.7444	Intermediate Similarity	NPC233649
0.7444	Intermediate Similarity	NPC470028
0.7442	Intermediate Similarity	NPC22918
0.7442	Intermediate Similarity	NPC473472
0.7442	Intermediate Similarity	NPC131466
0.7416	Intermediate Similarity	NPC473065
0.7416	Intermediate Similarity	NPC473067
0.7416	Intermediate Similarity	NPC473064
0.7412	Intermediate Similarity	NPC258501
0.7412	Intermediate Similarity	NPC43912
0.7412	Intermediate Similarity	NPC140446
0.7397	Intermediate Similarity	NPC165069
0.7386	Intermediate Similarity	NPC249204
0.7386	Intermediate Similarity	NPC325828
0.7386	Intermediate Similarity	NPC177834
0.7386	Intermediate Similarity	NPC137004
0.7386	Intermediate Similarity	NPC167644
0.7386	Intermediate Similarity	NPC477451
0.7386	Intermediate Similarity	NPC141769
0.7386	Intermediate Similarity	NPC172838
0.7386	Intermediate Similarity	NPC477547
0.7386	Intermediate Similarity	NPC48339
0.7386	Intermediate Similarity	NPC311246
0.7386	Intermediate Similarity	NPC88962
0.7386	Intermediate Similarity	NPC250393
0.7386	Intermediate Similarity	NPC297348
0.7386	Intermediate Similarity	NPC473726
0.7386	Intermediate Similarity	NPC144790
0.7386	Intermediate Similarity	NPC149400
0.7386	Intermediate Similarity	NPC234352
0.7375	Intermediate Similarity	NPC177343
0.7375	Intermediate Similarity	NPC272841
0.7368	Intermediate Similarity	NPC471879
0.7356	Intermediate Similarity	NPC473542
0.7333	Intermediate Similarity	NPC139271
0.7333	Intermediate Similarity	NPC304011
0.7333	Intermediate Similarity	NPC473287
0.7333	Intermediate Similarity	NPC476510
0.7333	Intermediate Similarity	NPC142264
0.7308	Intermediate Similarity	NPC200167
0.7308	Intermediate Similarity	NPC209666
0.7308	Intermediate Similarity	NPC31046
0.7308	Intermediate Similarity	NPC53868
0.7303	Intermediate Similarity	NPC3538
0.7303	Intermediate Similarity	NPC131693
0.7303	Intermediate Similarity	NPC179859
0.7303	Intermediate Similarity	NPC113500
0.7303	Intermediate Similarity	NPC475325
0.7303	Intermediate Similarity	NPC174024
0.7303	Intermediate Similarity	NPC471464
0.7303	Intermediate Similarity	NPC475436
0.7303	Intermediate Similarity	NPC175
0.7303	Intermediate Similarity	NPC312678
0.7303	Intermediate Similarity	NPC473503
0.7303	Intermediate Similarity	NPC30687
0.7303	Intermediate Similarity	NPC253268
0.7303	Intermediate Similarity	NPC24960
0.7303	Intermediate Similarity	NPC477224
0.7303	Intermediate Similarity	NPC291203
0.7303	Intermediate Similarity	NPC217205
0.7303	Intermediate Similarity	NPC264101
0.7303	Intermediate Similarity	NPC473851
0.7303	Intermediate Similarity	NPC291547
0.7303	Intermediate Similarity	NPC222731
0.7303	Intermediate Similarity	NPC473774
0.7303	Intermediate Similarity	NPC294686
0.7273	Intermediate Similarity	NPC210759
0.7273	Intermediate Similarity	NPC5632
0.7273	Intermediate Similarity	NPC149966
0.7273	Intermediate Similarity	NPC473637
0.7273	Intermediate Similarity	NPC229801
0.7273	Intermediate Similarity	NPC476668
0.7273	Intermediate Similarity	NPC276298
0.7273	Intermediate Similarity	NPC307167
0.726	Intermediate Similarity	NPC199937
0.7253	Intermediate Similarity	NPC477223
0.7253	Intermediate Similarity	NPC470684
0.7253	Intermediate Similarity	NPC470683
0.7253	Intermediate Similarity	NPC477222
0.7253	Intermediate Similarity	NPC210157
0.7241	Intermediate Similarity	NPC228059
0.7241	Intermediate Similarity	NPC20822
0.7241	Intermediate Similarity	NPC82955
0.7222	Intermediate Similarity	NPC473727
0.7222	Intermediate Similarity	NPC19400
0.7222	Intermediate Similarity	NPC6295
0.7222	Intermediate Similarity	NPC469710
0.7222	Intermediate Similarity	NPC215570
0.7222	Intermediate Similarity	NPC107188
0.7222	Intermediate Similarity	NPC475351
0.7222	Intermediate Similarity	NPC473610
0.7222	Intermediate Similarity	NPC107962
0.7222	Intermediate Similarity	NPC206003
0.7222	Intermediate Similarity	NPC211354
0.7209	Intermediate Similarity	NPC210658
0.7209	Intermediate Similarity	NPC161928
0.7204	Intermediate Similarity	NPC476838
0.7204	Intermediate Similarity	NPC476839
0.72	Intermediate Similarity	NPC179823
0.7191	Intermediate Similarity	NPC476669
0.7183	Intermediate Similarity	NPC475968
0.7174	Intermediate Similarity	NPC291548
0.7143	Intermediate Similarity	NPC121453
0.7143	Intermediate Similarity	NPC160426
0.7143	Intermediate Similarity	NPC98018
0.7143	Intermediate Similarity	NPC473601
0.7143	Intermediate Similarity	NPC30856
0.7143	Intermediate Similarity	NPC475625
0.7143	Intermediate Similarity	NPC470863
0.7143	Intermediate Similarity	NPC184617
0.7143	Intermediate Similarity	NPC219040
0.7143	Intermediate Similarity	NPC103616
0.7143	Intermediate Similarity	NPC470864
0.7143	Intermediate Similarity	NPC296936
0.7143	Intermediate Similarity	NPC287483
0.7143	Intermediate Similarity	NPC132080
0.7143	Intermediate Similarity	NPC470866
0.7143	Intermediate Similarity	NPC84111
0.7143	Intermediate Similarity	NPC475643
0.7143	Intermediate Similarity	NPC119425
0.7143	Intermediate Similarity	NPC97700
0.7143	Intermediate Similarity	NPC284104
0.7143	Intermediate Similarity	NPC116756
0.7143	Intermediate Similarity	NPC470865
0.7143	Intermediate Similarity	NPC232037
0.7143	Intermediate Similarity	NPC195297
0.7143	Intermediate Similarity	NPC128572
0.7128	Intermediate Similarity	NPC310138
0.7128	Intermediate Similarity	NPC114700
0.7128	Intermediate Similarity	NPC470029
0.7128	Intermediate Similarity	NPC134967
0.7126	Intermediate Similarity	NPC128475
0.7126	Intermediate Similarity	NPC470009
0.7111	Intermediate Similarity	NPC305418
0.7093	Intermediate Similarity	NPC471240
0.7093	Intermediate Similarity	NPC107603
0.7083	Intermediate Similarity	NPC477757
0.7083	Intermediate Similarity	NPC477755
0.7083	Intermediate Similarity	NPC477762
0.7083	Intermediate Similarity	NPC477753
0.7083	Intermediate Similarity	NPC477750
0.7083	Intermediate Similarity	NPC477763
0.7083	Intermediate Similarity	NPC472026
0.7079	Intermediate Similarity	NPC294643
0.7079	Intermediate Similarity	NPC274274
0.7079	Intermediate Similarity	NPC473150
0.7065	Intermediate Similarity	NPC470862
0.7065	Intermediate Similarity	NPC83137
0.7065	Intermediate Similarity	NPC115165

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 NPC470659 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	411
0.1-0.2	4395
0.2-0.3	3070
0.3-0.4	652
0.4-0.5	374
0.5-0.6	194
0.6-0.7	51
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
0.7386	Intermediate Similarity	NPD8171	Discontinued
0.7308	Intermediate Similarity	NPD1810	Approved
0.7308	Intermediate Similarity	NPD1811	Approved
0.7027	Intermediate Similarity	NPD371	Approved
0.6988	Remote Similarity	NPD6928	Phase 2
0.6812	Remote Similarity	NPD888	Phase 3
0.6812	Remote Similarity	NPD893	Approved
0.6812	Remote Similarity	NPD890	Clinical (unspecified phase)
0.6812	Remote Similarity	NPD891	Phase 3
0.6812	Remote Similarity	NPD892	Phase 3
0.6709	Remote Similarity	NPD2686	Approved
0.6709	Remote Similarity	NPD2254	Approved
0.6709	Remote Similarity	NPD2687	Approved
0.6633	Remote Similarity	NPD8170	Clinical (unspecified phase)
0.6571	Remote Similarity	NPD889	Approved
0.6571	Remote Similarity	NPD894	Approved
0.6571	Remote Similarity	NPD895	Approved
0.6571	Remote Similarity	NPD887	Approved
0.6528	Remote Similarity	NPD2267	Suspended
0.6522	Remote Similarity	NPD905	Approved
0.6522	Remote Similarity	NPD904	Phase 3
0.65	Remote Similarity	NPD7532	Clinical (unspecified phase)
0.6364	Remote Similarity	NPD3669	Approved
0.6364	Remote Similarity	NPD3670	Clinical (unspecified phase)
0.63	Remote Similarity	NPD4057	Clinical (unspecified phase)
0.63	Remote Similarity	NPD4056	Clinical (unspecified phase)
0.6197	Remote Similarity	NPD2269	Approved
0.6184	Remote Similarity	NPD6123	Approved
0.6176	Remote Similarity	NPD6412	Phase 2
0.6029	Remote Similarity	NPD9000	Phase 3
0.6029	Remote Similarity	NPD8998	Phase 2
0.6029	Remote Similarity	NPD8993	Phase 1
0.6029	Remote Similarity	NPD8999	Phase 3
0.6029	Remote Similarity	NPD8997	Approved
0.5981	Remote Similarity	NPD8133	Approved
0.5977	Remote Similarity	NPD4238	Approved
0.5977	Remote Similarity	NPD4802	Phase 2
0.5976	Remote Similarity	NPD4267	Clinical (unspecified phase)
0.5955	Remote Similarity	NPD1780	Approved
0.5955	Remote Similarity	NPD1779	Approved
0.5946	Remote Similarity	NPD8377	Approved
0.5946	Remote Similarity	NPD8294	Approved
0.5909	Remote Similarity	NPD7328	Approved
0.5909	Remote Similarity	NPD7327	Approved
0.5893	Remote Similarity	NPD8380	Approved
0.5893	Remote Similarity	NPD8033	Approved
0.5893	Remote Similarity	NPD8296	Approved
0.5893	Remote Similarity	NPD8379	Approved
0.5893	Remote Similarity	NPD8335	Approved
0.5893	Remote Similarity	NPD8378	Approved
0.5857	Remote Similarity	NPD8966	Approved
0.5857	Remote Similarity	NPD8965	Approved
0.5856	Remote Similarity	NPD7516	Approved
0.5823	Remote Similarity	NPD847	Phase 1
0.5816	Remote Similarity	NPD7991	Discontinued
0.5814	Remote Similarity	NPD3702	Approved
0.5811	Remote Similarity	NPD7346	Approved
0.5789	Remote Similarity	NPD369	Approved
0.5784	Remote Similarity	NPD8083	Approved
0.5784	Remote Similarity	NPD8139	Approved
0.5784	Remote Similarity	NPD8138	Approved
0.5784	Remote Similarity	NPD8085	Approved
0.5784	Remote Similarity	NPD8084	Approved
0.5784	Remote Similarity	NPD8082	Approved
0.5784	Remote Similarity	NPD8086	Approved
0.5752	Remote Similarity	NPD7503	Approved
0.5745	Remote Similarity	NPD7524	Approved
0.5728	Remote Similarity	NPD8276	Approved
0.5728	Remote Similarity	NPD8275	Approved
0.5714	Remote Similarity	NPD4787	Phase 1
0.5673	Remote Similarity	NPD8081	Approved
0.5641	Remote Similarity	NPD3198	Approved
0.5619	Remote Similarity	NPD8393	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