NPASS Compound

Structure

Physi-Chem Properties

Molecular Weight:	526.21
Volume:	504.951
LogP:	-0.439
LogD:	-0.111
LogS:	-2.124
# Rotatable Bonds:	12
TPSA:	198.76
# H-Bond Aceptor:	12
# H-Bond Donor:	8
# Rings:	3
# Heavy Atoms:	12

MedChem Properties

QED Drug-Likeness Score:	0.163
Synthetic Accessibility Score:	4.224
Fsp3:	0.52
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	1
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.321
MDCK Permeability:	2.0777604731847532e-05
Pgp-inhibitor:	0.006
Pgp-substrate:	0.962
Human Intestinal Absorption (HIA):	0.953
20% Bioavailability (F20%):	0.111
30% Bioavailability (F30%):	0.997

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.147
Plasma Protein Binding (PPB):	79.5343246459961%
Volume Distribution (VD):	0.352
Pgp-substrate:	12.500447273254395%

ADMET: Metabolism

CYP1A2-inhibitor:	0.035
CYP1A2-substrate:	0.053
CYP2C19-inhibitor:	0.017
CYP2C19-substrate:	0.251
CYP2C9-inhibitor:	0.005
CYP2C9-substrate:	0.295
CYP2D6-inhibitor:	0.07
CYP2D6-substrate:	0.184
CYP3A4-inhibitor:	0.025
CYP3A4-substrate:	0.072

ADMET: Excretion

Clearance (CL):	4.05
Half-life (T1/2):	0.841

ADMET: Toxicity

hERG Blockers:	0.295
Human Hepatotoxicity (H-HT):	0.13
Drug-inuced Liver Injury (DILI):	0.043
AMES Toxicity:	0.137
Rat Oral Acute Toxicity:	0.008
Maximum Recommended Daily Dose:	0.003
Skin Sensitization:	0.62
Carcinogencity:	0.043
Eye Corrosion:	0.003
Eye Irritation:	0.02
Respiratory Toxicity:	0.006

Download Data

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

Natural Product: NPC138647

Natural Product ID:	NPC138647
*Common Name:**	SSZZFAJCDFWCJW-JCJKHTMNSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	SSZZFAJCDFWCJW-JCJKHTMNSA-N
Standard InCHI:	InChI=1S/C15H20O4/c1-8-9-6-12-14(2,19-12)5-4-11-15(3,18-11)7-10(9)17-13(8)16/h9-12H,1,4-7H2,2-3H3/t9-,10+,11-,12-,14-,15-/m1/s1
SMILES:	O=C1O[C@@H]2[C@@H](C1=C)C[C@H]1O[C@]1(C)CC[C@@H]1[C@](C2)(C)O1
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL3623293
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001283] Terpene lactones

*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
NPO26335	Carpesium abrotanoides	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26316467]
NPO26335	Carpesium abrotanoides	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO26335	Carpesium abrotanoides	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO26335	Carpesium abrotanoides	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO26335	Carpesium abrotanoides	Species	Asteraceae	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	12
MIC	1

Activity Type	# Activity
Cell Line	9
NON-MOLECULAR	1
Organism	3

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT83	Cell Line	MCF7	Homo sapiens	IC50	=	4100.0	nM	PMID[493730]
NPT111	Cell Line	K562	Homo sapiens	IC50	=	1700.0	nM	PMID[493730]
NPT165	Cell Line	HeLa	Homo sapiens	IC50	=	1000.0	nM	PMID[493730]
NPT90	Cell Line	DU-145	Homo sapiens	IC50	=	380.0	nM	PMID[493730]
NPT466	Cell Line	U-937	Homo sapiens	IC50	=	210.0	nM	PMID[493730]
NPT2341	Cell Line	NCI-H1975	Homo sapiens	IC50	=	5400.0	nM	PMID[493730]
NPT81	Cell Line	A549	Homo sapiens	IC50	=	2000.0	nM	PMID[493730]
NPT112	Cell Line	MOLT-4	Homo sapiens	IC50	=	1200.0	nM	PMID[493730]
NPT116	Cell Line	HL-60	Homo sapiens	IC50	=	180.0	nM	PMID[493730]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	IC50	=	6400.0	nM	PMID[493730]
NPT742	Organism	Influenza A virus	Influenza A virus	IC50	=	10800.0	nM	PMID[493730]
NPT742	Organism	Influenza A virus	Influenza A virus	IC50	=	11600.0	nM	PMID[493730]
NPT115	Organism	Mycobacterium tuberculosis H37Ra	Mycobacterium tuberculosis H37Ra	MIC	=	6000.0	nM	PMID[493730]

☑ 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 NPC138647 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	274
0.1-0.2	2458
0.2-0.3	7957
0.3-0.4	16419
0.4-0.5	9598
0.5-0.6	4543
0.6-0.7	1155
0.7-0.8	247
0.8-0.85	38
0.85-0.9	4
0.9-0.95	2
0.95-1	2

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC470238
0.9176	High Similarity	NPC70251
0.9176	High Similarity	NPC475881
0.9157	High Similarity	NPC5130
0.8721	High Similarity	NPC166919
0.8721	High Similarity	NPC151770
0.8675	High Similarity	NPC128429
0.8675	High Similarity	NPC272814
0.8588	High Similarity	NPC50637
0.8588	High Similarity	NPC470242
0.8571	High Similarity	NPC474213
0.8539	High Similarity	NPC471147
0.8488	Intermediate Similarity	NPC231889
0.8471	Intermediate Similarity	NPC50362
0.8471	Intermediate Similarity	NPC319795
0.8471	Intermediate Similarity	NPC38468
0.8452	Intermediate Similarity	NPC257358
0.8452	Intermediate Similarity	NPC474472
0.8409	Intermediate Similarity	NPC475748
0.8409	Intermediate Similarity	NPC312042
0.837	Intermediate Similarity	NPC208233
0.8352	Intermediate Similarity	NPC35498
0.8333	Intermediate Similarity	NPC473316
0.8333	Intermediate Similarity	NPC473330
0.8333	Intermediate Similarity	NPC140543
0.8276	Intermediate Similarity	NPC475703
0.8276	Intermediate Similarity	NPC270270
0.8256	Intermediate Similarity	NPC304509
0.8256	Intermediate Similarity	NPC474547
0.8256	Intermediate Similarity	NPC47958
0.8256	Intermediate Similarity	NPC149725
0.8222	Intermediate Similarity	NPC212486
0.8214	Intermediate Similarity	NPC141810
0.8202	Intermediate Similarity	NPC62815
0.8202	Intermediate Similarity	NPC469718
0.8202	Intermediate Similarity	NPC251385
0.8202	Intermediate Similarity	NPC329857
0.8202	Intermediate Similarity	NPC49342
0.8193	Intermediate Similarity	NPC80999
0.8193	Intermediate Similarity	NPC617
0.8191	Intermediate Similarity	NPC477511
0.8191	Intermediate Similarity	NPC264477
0.8132	Intermediate Similarity	NPC476267
0.8132	Intermediate Similarity	NPC57405
0.8132	Intermediate Similarity	NPC190294
0.8132	Intermediate Similarity	NPC303942
0.8111	Intermediate Similarity	NPC20713
0.8095	Intermediate Similarity	NPC474981
0.809	Intermediate Similarity	NPC472872
0.8068	Intermediate Similarity	NPC118601
0.8068	Intermediate Similarity	NPC186148
0.8065	Intermediate Similarity	NPC471140
0.8043	Intermediate Similarity	NPC14961
0.8043	Intermediate Similarity	NPC475659
0.8043	Intermediate Similarity	NPC476053
0.8043	Intermediate Similarity	NPC270013
0.8022	Intermediate Similarity	NPC125674
0.8022	Intermediate Similarity	NPC475838
0.8022	Intermediate Similarity	NPC228451
0.8	Intermediate Similarity	NPC47635
0.8	Intermediate Similarity	NPC201718
0.7979	Intermediate Similarity	NPC279561
0.7979	Intermediate Similarity	NPC473326
0.7978	Intermediate Similarity	NPC202672
0.7978	Intermediate Similarity	NPC178875
0.7978	Intermediate Similarity	NPC224652
0.7978	Intermediate Similarity	NPC58219
0.7978	Intermediate Similarity	NPC177629
0.7957	Intermediate Similarity	NPC476315
0.7957	Intermediate Similarity	NPC473859
0.7957	Intermediate Similarity	NPC31645
0.7957	Intermediate Similarity	NPC39859
0.7957	Intermediate Similarity	NPC76862
0.7957	Intermediate Similarity	NPC470883
0.7957	Intermediate Similarity	NPC158416
0.7955	Intermediate Similarity	NPC162071
0.7938	Intermediate Similarity	NPC477510
0.7938	Intermediate Similarity	NPC471143
0.7935	Intermediate Similarity	NPC81386
0.7935	Intermediate Similarity	NPC474247
0.7935	Intermediate Similarity	NPC474035
0.7912	Intermediate Similarity	NPC155215
0.7912	Intermediate Similarity	NPC184463
0.7907	Intermediate Similarity	NPC246076
0.7895	Intermediate Similarity	NPC288876
0.7895	Intermediate Similarity	NPC477512
0.7889	Intermediate Similarity	NPC92974
0.7889	Intermediate Similarity	NPC307411
0.7889	Intermediate Similarity	NPC4986
0.7872	Intermediate Similarity	NPC328562
0.7872	Intermediate Similarity	NPC323421
0.7872	Intermediate Similarity	NPC474921
0.7865	Intermediate Similarity	NPC190753
0.7857	Intermediate Similarity	NPC23187
0.7849	Intermediate Similarity	NPC474947
0.7849	Intermediate Similarity	NPC56369
0.7826	Intermediate Similarity	NPC258216
0.7826	Intermediate Similarity	NPC476300
0.7826	Intermediate Similarity	NPC475912
0.7802	Intermediate Similarity	NPC51004
0.7791	Intermediate Similarity	NPC207188
0.7789	Intermediate Similarity	NPC45125
0.7778	Intermediate Similarity	NPC79549
0.7778	Intermediate Similarity	NPC477513
0.7766	Intermediate Similarity	NPC476275
0.7766	Intermediate Similarity	NPC230800
0.7766	Intermediate Similarity	NPC17585
0.7766	Intermediate Similarity	NPC279621
0.7753	Intermediate Similarity	NPC475019
0.7753	Intermediate Similarity	NPC476015
0.7753	Intermediate Similarity	NPC474762
0.7753	Intermediate Similarity	NPC304558
0.7753	Intermediate Similarity	NPC284902
0.7753	Intermediate Similarity	NPC474949
0.7742	Intermediate Similarity	NPC66581
0.7732	Intermediate Similarity	NPC471148
0.7727	Intermediate Similarity	NPC474780
0.7717	Intermediate Similarity	NPC12172
0.7717	Intermediate Similarity	NPC191339
0.7717	Intermediate Similarity	NPC286341
0.7717	Intermediate Similarity	NPC30515
0.7717	Intermediate Similarity	NPC208886
0.7711	Intermediate Similarity	NPC471491
0.7708	Intermediate Similarity	NPC471381
0.7708	Intermediate Similarity	NPC186861
0.7692	Intermediate Similarity	NPC215556
0.7667	Intermediate Similarity	NPC24728
0.766	Intermediate Similarity	NPC471141
0.766	Intermediate Similarity	NPC475900
0.766	Intermediate Similarity	NPC163228
0.766	Intermediate Similarity	NPC36954
0.764	Intermediate Similarity	NPC329749
0.764	Intermediate Similarity	NPC235792
0.7634	Intermediate Similarity	NPC179746
0.7634	Intermediate Similarity	NPC81419
0.7634	Intermediate Similarity	NPC153590
0.7634	Intermediate Similarity	NPC135776
0.7629	Intermediate Similarity	NPC15993
0.7629	Intermediate Similarity	NPC475958
0.7629	Intermediate Similarity	NPC476270
0.7619	Intermediate Similarity	NPC235906
0.7614	Intermediate Similarity	NPC475842
0.7614	Intermediate Similarity	NPC170377
0.7614	Intermediate Similarity	NPC54468
0.7609	Intermediate Similarity	NPC474323
0.7609	Intermediate Similarity	NPC216284
0.7609	Intermediate Similarity	NPC179394
0.7609	Intermediate Similarity	NPC206614
0.7609	Intermediate Similarity	NPC144133
0.7609	Intermediate Similarity	NPC475855
0.7586	Intermediate Similarity	NPC281949
0.7586	Intermediate Similarity	NPC25684
0.7586	Intermediate Similarity	NPC301477
0.7582	Intermediate Similarity	NPC217983
0.7582	Intermediate Similarity	NPC473715
0.7582	Intermediate Similarity	NPC207114
0.7582	Intermediate Similarity	NPC471149
0.7579	Intermediate Similarity	NPC476009
0.7558	Intermediate Similarity	NPC19841
0.7556	Intermediate Similarity	NPC475491
0.7556	Intermediate Similarity	NPC238593
0.7556	Intermediate Similarity	NPC204048
0.7556	Intermediate Similarity	NPC309757
0.7556	Intermediate Similarity	NPC469626
0.7556	Intermediate Similarity	NPC64153
0.7556	Intermediate Similarity	NPC469676
0.7556	Intermediate Similarity	NPC187661
0.7556	Intermediate Similarity	NPC236692
0.7551	Intermediate Similarity	NPC324017
0.7551	Intermediate Similarity	NPC320019
0.7529	Intermediate Similarity	NPC141789
0.7529	Intermediate Similarity	NPC208223
0.7529	Intermediate Similarity	NPC171204
0.7529	Intermediate Similarity	NPC476028
0.7529	Intermediate Similarity	NPC476794
0.7529	Intermediate Similarity	NPC470240
0.7528	Intermediate Similarity	NPC151176
0.7528	Intermediate Similarity	NPC3464
0.7528	Intermediate Similarity	NPC114979
0.7528	Intermediate Similarity	NPC191476
0.7528	Intermediate Similarity	NPC475963
0.7527	Intermediate Similarity	NPC133698
0.7527	Intermediate Similarity	NPC184063
0.7527	Intermediate Similarity	NPC131209
0.75	Intermediate Similarity	NPC283409
0.75	Intermediate Similarity	NPC474951
0.75	Intermediate Similarity	NPC173926
0.75	Intermediate Similarity	NPC155935
0.75	Intermediate Similarity	NPC474032
0.75	Intermediate Similarity	NPC155587
0.75	Intermediate Similarity	NPC471150
0.75	Intermediate Similarity	NPC295312
0.7471	Intermediate Similarity	NPC293418
0.7471	Intermediate Similarity	NPC474510
0.7471	Intermediate Similarity	NPC73052
0.7471	Intermediate Similarity	NPC290508
0.7471	Intermediate Similarity	NPC223904
0.7451	Intermediate Similarity	NPC59489
0.7451	Intermediate Similarity	NPC139838
0.7449	Intermediate Similarity	NPC473332

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 NPC138647 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	314
0.1-0.2	3082
0.2-0.3	3782
0.3-0.4	1412
0.4-0.5	440
0.5-0.6	109
0.6-0.7	9
0.7-0.8	1
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
0.8471	Intermediate Similarity	NPD1733	Clinical (unspecified phase)
0.7889	Intermediate Similarity	NPD1695	Approved
0.6939	Remote Similarity	NPD1698	Clinical (unspecified phase)
0.6875	Remote Similarity	NPD46	Approved
0.6875	Remote Similarity	NPD6698	Approved
0.6604	Remote Similarity	NPD7899	Clinical (unspecified phase)
0.6531	Remote Similarity	NPD7838	Discovery
0.6509	Remote Similarity	NPD6008	Approved
0.6449	Remote Similarity	NPD5954	Clinical (unspecified phase)
0.6422	Remote Similarity	NPD6371	Approved
0.6354	Remote Similarity	NPD1694	Approved
0.6346	Remote Similarity	NPD6648	Approved
0.63	Remote Similarity	NPD7983	Approved
0.6286	Remote Similarity	NPD5344	Discontinued
0.6273	Remote Similarity	NPD5955	Clinical (unspecified phase)
0.6235	Remote Similarity	NPD2685	Clinical (unspecified phase)
0.6211	Remote Similarity	NPD4752	Clinical (unspecified phase)
0.6182	Remote Similarity	NPD4061	Clinical (unspecified phase)
0.6176	Remote Similarity	NPD5282	Discontinued
0.6161	Remote Similarity	NPD6053	Discontinued
0.6078	Remote Similarity	NPD5778	Approved
0.6078	Remote Similarity	NPD5779	Approved
0.6071	Remote Similarity	NPD8413	Clinical (unspecified phase)
0.6042	Remote Similarity	NPD6435	Approved
0.5979	Remote Similarity	NPD7154	Phase 3
0.596	Remote Similarity	NPD4249	Approved
0.5946	Remote Similarity	NPD6686	Approved
0.5943	Remote Similarity	NPD8029	Clinical (unspecified phase)
0.59	Remote Similarity	NPD4250	Approved
0.59	Remote Similarity	NPD4251	Approved
0.5882	Remote Similarity	NPD5785	Approved
0.5876	Remote Similarity	NPD5209	Approved
0.5833	Remote Similarity	NPD5368	Approved
0.5804	Remote Similarity	NPD5345	Clinical (unspecified phase)
0.58	Remote Similarity	NPD5786	Approved
0.5794	Remote Similarity	NPD4225	Approved
0.5784	Remote Similarity	NPD6101	Approved
0.5784	Remote Similarity	NPD5764	Clinical (unspecified phase)
0.5773	Remote Similarity	NPD5369	Approved
0.5755	Remote Similarity	NPD7839	Suspended
0.575	Remote Similarity	NPD8513	Phase 3
0.575	Remote Similarity	NPD8515	Approved
0.575	Remote Similarity	NPD8516	Approved
0.575	Remote Similarity	NPD8517	Approved
0.57	Remote Similarity	NPD6082	Clinical (unspecified phase)
0.57	Remote Similarity	NPD5363	Approved
0.5678	Remote Similarity	NPD7115	Discovery
0.5673	Remote Similarity	NPD6411	Approved
0.567	Remote Similarity	NPD4821	Approved
0.567	Remote Similarity	NPD4820	Approved
0.567	Remote Similarity	NPD5790	Clinical (unspecified phase)
0.567	Remote Similarity	NPD4822	Approved
0.567	Remote Similarity	NPD4819	Approved
0.5657	Remote Similarity	NPD5362	Discontinued
0.5656	Remote Similarity	NPD7642	Approved
0.5648	Remote Similarity	NPD7638	Approved
0.5638	Remote Similarity	NPD8039	Approved
0.5619	Remote Similarity	NPD6399	Phase 3

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