NPASS Compound

Structure

NPC181204 OpenBabel07101718332D 30 33 0 0 1 0 0 0 0 0999 V2000 -4.8126 -3.7859 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1653 -4.3212 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1945 -1.8838 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5909 -2.0032 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4067 -0.9135 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5472 -2.4190 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2382 -1.4680 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5388 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8344 -3.5780 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5254 -2.6270 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.2601 -1.2601 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.5981 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 1.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.9511 -0.3090 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.9511 1.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 1.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.0000 -0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 5.1962 3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.2601 2.2601 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 17 1 0 0 0 0 2 17 1 0 0 0 0 7 8 2 0 0 0 0 7 18 1 0 0 0 0 8 19 1 0 0 0 0 9 10 2 0 0 0 0 9 20 1 0 0 0 0 10 22 1 0 0 0 0 11 13 1 0 0 0 0 11 21 1 0 0 0 0 12 14 1 0 0 0 0 12 23 1 0 0 0 0 13 27 1 0 0 0 0 14 28 1 0 0 0 0 15 20 2 0 0 0 0 15 21 1 0 0 0 0 16 24 1 0 0 0 0 16 25 1 0 0 0 0 17 18 1 0 0 0 0 18 3 1 1 0 0 0 19 4 1 6 0 0 0 19 24 1 0 0 0 0 20 27 1 0 0 0 0 21 29 2 0 0 0 0 22 23 1 0 0 0 0 22 26 2 0 0 0 0 23 27 1 1 0 0 0 24 28 1 1 0 0 0 25 26 1 0 0 0 0 25 30 2 0 0 0 0 26 28 1 0 0 0 0 27 5 1 1 0 0 0 28 6 1 1 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	406.29
Volume:	460.38
LogP:	5.606
LogD:	4.326
LogS:	-6.435
# Rotatable Bonds:	4
TPSA:	34.14
# H-Bond Aceptor:	2
# H-Bond Donor:	0
# Rings:	4
# Heavy Atoms:	2

MedChem Properties

QED Drug-Likeness Score:	0.491
Synthetic Accessibility Score:	4.884
Fsp3:	0.643
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:	-4.952
MDCK Permeability:	1.8098049622494727e-05
Pgp-inhibitor:	1.0
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.014
20% Bioavailability (F20%):	0.908
30% Bioavailability (F30%):	0.274

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.003
Plasma Protein Binding (PPB):	93.2009048461914%
Volume Distribution (VD):	1.335
Pgp-substrate:	2.6720340251922607%

ADMET: Metabolism

CYP1A2-inhibitor:	0.078
CYP1A2-substrate:	0.772
CYP2C19-inhibitor:	0.71
CYP2C19-substrate:	0.942
CYP2C9-inhibitor:	0.719
CYP2C9-substrate:	0.088
CYP2D6-inhibitor:	0.121
CYP2D6-substrate:	0.197
CYP3A4-inhibitor:	0.925
CYP3A4-substrate:	0.921

ADMET: Excretion

Clearance (CL):	0.956
Half-life (T1/2):	0.178

ADMET: Toxicity

hERG Blockers:	0.321
Human Hepatotoxicity (H-HT):	0.213
Drug-inuced Liver Injury (DILI):	0.351
AMES Toxicity:	0.035
Rat Oral Acute Toxicity:	0.638
Maximum Recommended Daily Dose:	0.948
Skin Sensitization:	0.943
Carcinogencity:	0.032
Eye Corrosion:	0.003
Eye Irritation:	0.036
Respiratory Toxicity:	0.933

Download Data

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

Natural Product: NPC181204

Natural Product ID:	NPC181204
*Common Name:**	Gymnasterone D
IUPAC Name:	(9R,10R,13R,17R)-17-[(E,2R,5R)-5,6-dimethylhept-3-en-2-yl]-10,13-dimethyl-2,9,11,12,16,17-hexahydro-1H-cyclopenta[a]phenanthrene-3,15-dione
Synonyms:	Gymnasterone D
Standard InCHIKey:	GQXHQDCLIABAJK-FYQXRWMHSA-N
Standard InCHI:	InChI=1S/C28H38O2/c1-17(2)18(3)7-8-19(4)24-16-25(30)26-22-10-9-20-15-21(29)11-13-27(20,5)23(22)12-14-28(24,26)6/h7-10,15,17-19,23-24H,11-14,16H2,1-6H3/b8-7+/t18-,19+,23-,24+,27-,28+/m0/s1
SMILES:	CC([C@H](/C=C/[C@H]([C@H]1CC(=O)C2=C3[C@H](CC[C@]12C)[C@@]1(C)CCC(=O)C=C1C=C3)C)C)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL401060
PubChem CID:	24179452
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0003567] Ergostane steroids [CHEMONTID:0001403] Ergosterols 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
NPO33119	gymnascella dankaliensis	Species	Gymnoascaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[17067147]
NPO33119	gymnascella dankaliensis	Species	Gymnoascaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[17988094]
NPO33119	gymnascella dankaliensis	Species	Gymnoascaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18284207]
NPO33119	gymnascella dankaliensis	Species	Gymnoascaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[25600409]

☑ 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
ED50	1

Activity Type	# Activity
Cell Line	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT168	Cell Line	P388	Mus musculus	ED50	=	2.5	ug ml-1	PMID[512778]

☑ 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 NPC181204 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	183
0.1-0.2	1719
0.2-0.3	11642
0.3-0.4	15508
0.4-0.5	8521
0.5-0.6	3905
0.6-0.7	1025
0.7-0.8	168
0.8-0.85	22
0.85-0.9	3
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
0.875	High Similarity	NPC473171
0.8732	High Similarity	NPC470045
0.8732	High Similarity	NPC470044
0.8696	High Similarity	NPC87141
0.8657	High Similarity	NPC4638
0.8611	High Similarity	NPC474797
0.8611	High Similarity	NPC329866
0.8611	High Similarity	NPC474796
0.8611	High Similarity	NPC309852
0.8592	High Similarity	NPC115023
0.8592	High Similarity	NPC54123
0.8592	High Similarity	NPC470078
0.8571	High Similarity	NPC139397
0.8571	High Similarity	NPC256846
0.8533	High Similarity	NPC170793
0.8472	Intermediate Similarity	NPC474228
0.8472	Intermediate Similarity	NPC251705
0.8472	Intermediate Similarity	NPC303613
0.8451	Intermediate Similarity	NPC251929
0.8451	Intermediate Similarity	NPC2634
0.8451	Intermediate Similarity	NPC159577
0.8451	Intermediate Similarity	NPC35734
0.8451	Intermediate Similarity	NPC265782
0.8451	Intermediate Similarity	NPC307176
0.8451	Intermediate Similarity	NPC260040
0.8451	Intermediate Similarity	NPC282593
0.8429	Intermediate Similarity	NPC188292
0.8429	Intermediate Similarity	NPC260474
0.8429	Intermediate Similarity	NPC310992
0.8382	Intermediate Similarity	NPC212210
0.8378	Intermediate Similarity	NPC69408
0.8333	Intermediate Similarity	NPC305501
0.8333	Intermediate Similarity	NPC5701
0.8333	Intermediate Similarity	NPC259261
0.8333	Intermediate Similarity	NPC234707
0.831	Intermediate Similarity	NPC182815
0.8261	Intermediate Similarity	NPC251118
0.8243	Intermediate Similarity	NPC293803
0.8235	Intermediate Similarity	NPC288253
0.8182	Intermediate Similarity	NPC266295
0.8182	Intermediate Similarity	NPC94991
0.8169	Intermediate Similarity	NPC20610
0.8148	Intermediate Similarity	NPC287079
0.8143	Intermediate Similarity	NPC323005
0.8133	Intermediate Similarity	NPC469796
0.8133	Intermediate Similarity	NPC469793
0.8108	Intermediate Similarity	NPC255021
0.8088	Intermediate Similarity	NPC213152
0.8082	Intermediate Similarity	NPC223187
0.8052	Intermediate Similarity	NPC90965
0.803	Intermediate Similarity	NPC230823
0.8028	Intermediate Similarity	NPC475523
0.8	Intermediate Similarity	NPC87552
0.8	Intermediate Similarity	NPC255650
0.7971	Intermediate Similarity	NPC202118
0.7971	Intermediate Similarity	NPC197238
0.7971	Intermediate Similarity	NPC32285
0.7971	Intermediate Similarity	NPC165695
0.7949	Intermediate Similarity	NPC474509
0.7945	Intermediate Similarity	NPC40574
0.7941	Intermediate Similarity	NPC25853
0.7941	Intermediate Similarity	NPC127582
0.7922	Intermediate Similarity	NPC469996
0.7857	Intermediate Similarity	NPC473902
0.7857	Intermediate Similarity	NPC469662
0.7848	Intermediate Similarity	NPC4166
0.7838	Intermediate Similarity	NPC190035
0.7831	Intermediate Similarity	NPC320665
0.7778	Intermediate Similarity	NPC176107
0.7761	Intermediate Similarity	NPC267626
0.7761	Intermediate Similarity	NPC55004
0.7761	Intermediate Similarity	NPC49575
0.775	Intermediate Similarity	NPC469804
0.775	Intermediate Similarity	NPC3511
0.775	Intermediate Similarity	NPC142253
0.775	Intermediate Similarity	NPC469805
0.775	Intermediate Similarity	NPC311092
0.7727	Intermediate Similarity	NPC470893
0.7711	Intermediate Similarity	NPC136548
0.7703	Intermediate Similarity	NPC477856
0.7703	Intermediate Similarity	NPC214770
0.7692	Intermediate Similarity	NPC189485
0.7692	Intermediate Similarity	NPC470052
0.7692	Intermediate Similarity	NPC82635
0.7671	Intermediate Similarity	NPC155198
0.7662	Intermediate Similarity	NPC1254
0.7654	Intermediate Similarity	NPC83569
0.7654	Intermediate Similarity	NPC3856
0.7654	Intermediate Similarity	NPC279639
0.7654	Intermediate Similarity	NPC41539
0.7654	Intermediate Similarity	NPC474976
0.7654	Intermediate Similarity	NPC69279
0.7654	Intermediate Similarity	NPC474790
0.7647	Intermediate Similarity	NPC30215
0.7647	Intermediate Similarity	NPC27610
0.7647	Intermediate Similarity	NPC311852
0.7647	Intermediate Similarity	NPC56905
0.7639	Intermediate Similarity	NPC92327
0.7625	Intermediate Similarity	NPC225515
0.7625	Intermediate Similarity	NPC470034
0.7606	Intermediate Similarity	NPC285371
0.7606	Intermediate Similarity	NPC475124
0.76	Intermediate Similarity	NPC225467
0.7595	Intermediate Similarity	NPC27817
0.759	Intermediate Similarity	NPC222613
0.759	Intermediate Similarity	NPC475022
0.759	Intermediate Similarity	NPC118648
0.7571	Intermediate Similarity	NPC475795
0.7571	Intermediate Similarity	NPC97322
0.7571	Intermediate Similarity	NPC60565
0.7568	Intermediate Similarity	NPC286814
0.7564	Intermediate Similarity	NPC91665
0.7561	Intermediate Similarity	NPC473246
0.7558	Intermediate Similarity	NPC204341
0.7536	Intermediate Similarity	NPC143834
0.7536	Intermediate Similarity	NPC276764
0.7536	Intermediate Similarity	NPC472304
0.7534	Intermediate Similarity	NPC193770
0.7531	Intermediate Similarity	NPC472239
0.7531	Intermediate Similarity	NPC321289
0.7531	Intermediate Similarity	NPC320514
0.7531	Intermediate Similarity	NPC327969
0.7531	Intermediate Similarity	NPC469799
0.7531	Intermediate Similarity	NPC469806
0.75	Intermediate Similarity	NPC476293
0.75	Intermediate Similarity	NPC75315
0.75	Intermediate Similarity	NPC469798
0.75	Intermediate Similarity	NPC115385
0.75	Intermediate Similarity	NPC287063
0.75	Intermediate Similarity	NPC163016
0.75	Intermediate Similarity	NPC469797
0.747	Intermediate Similarity	NPC29447
0.747	Intermediate Similarity	NPC8571
0.747	Intermediate Similarity	NPC470048
0.747	Intermediate Similarity	NPC472931
0.747	Intermediate Similarity	NPC11711
0.747	Intermediate Similarity	NPC472940
0.7465	Intermediate Similarity	NPC167256
0.7442	Intermediate Similarity	NPC129913
0.7439	Intermediate Similarity	NPC470015
0.7439	Intermediate Similarity	NPC168188
0.7436	Intermediate Similarity	NPC110725
0.7436	Intermediate Similarity	NPC474463
0.7432	Intermediate Similarity	NPC82477
0.7432	Intermediate Similarity	NPC39157
0.7432	Intermediate Similarity	NPC142754
0.7432	Intermediate Similarity	NPC296697
0.7407	Intermediate Similarity	NPC475863
0.7407	Intermediate Similarity	NPC38350
0.7407	Intermediate Similarity	NPC201912
0.7407	Intermediate Similarity	NPC477372
0.7403	Intermediate Similarity	NPC219232
0.7403	Intermediate Similarity	NPC128346
0.7397	Intermediate Similarity	NPC176171
0.7361	Intermediate Similarity	NPC6697
0.7356	Intermediate Similarity	NPC19114
0.7349	Intermediate Similarity	NPC85774
0.7349	Intermediate Similarity	NPC214043
0.7349	Intermediate Similarity	NPC320801
0.7342	Intermediate Similarity	NPC470557
0.7333	Intermediate Similarity	NPC477857
0.7333	Intermediate Similarity	NPC161147
0.7326	Intermediate Similarity	NPC474844
0.7317	Intermediate Similarity	NPC472867
0.7317	Intermediate Similarity	NPC193347
0.7317	Intermediate Similarity	NPC260956
0.7317	Intermediate Similarity	NPC268122
0.7317	Intermediate Similarity	NPC100297
0.7308	Intermediate Similarity	NPC65650
0.7308	Intermediate Similarity	NPC476346
0.7303	Intermediate Similarity	NPC171395
0.7297	Intermediate Similarity	NPC220210
0.7297	Intermediate Similarity	NPC20181
0.7294	Intermediate Similarity	NPC58063
0.7294	Intermediate Similarity	NPC93778
0.7294	Intermediate Similarity	NPC141292
0.7273	Intermediate Similarity	NPC130016
0.7273	Intermediate Similarity	NPC180015
0.7273	Intermediate Similarity	NPC250575
0.7273	Intermediate Similarity	NPC109576
0.7273	Intermediate Similarity	NPC474488
0.7273	Intermediate Similarity	NPC276336
0.7273	Intermediate Similarity	NPC56747
0.7262	Intermediate Similarity	NPC469948
0.7262	Intermediate Similarity	NPC311702
0.7262	Intermediate Similarity	NPC94531
0.7262	Intermediate Similarity	NPC470574
0.7262	Intermediate Similarity	NPC123319
0.7262	Intermediate Similarity	NPC33881
0.726	Intermediate Similarity	NPC268039
0.725	Intermediate Similarity	NPC471409
0.725	Intermediate Similarity	NPC228911
0.725	Intermediate Similarity	NPC275494
0.725	Intermediate Similarity	NPC115515
0.7246	Intermediate Similarity	NPC192427
0.7237	Intermediate Similarity	NPC246722
0.7237	Intermediate Similarity	NPC151045
0.7229	Intermediate Similarity	NPC118423
0.7222	Intermediate Similarity	NPC472306
0.7215	Intermediate Similarity	NPC899

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 NPC181204 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	168
0.1-0.2	1987
0.2-0.3	4564
0.3-0.4	1765
0.4-0.5	362
0.5-0.6	213
0.6-0.7	69
0.7-0.8	17
0.8-0.85	2
0.85-0.9	3
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.9143	High Similarity	NPD4687	Approved
0.9143	High Similarity	NPD5733	Approved
0.913	High Similarity	NPD5276	Approved
0.8873	High Similarity	NPD4058	Approved
0.8571	High Similarity	NPD4137	Phase 3
0.8451	Intermediate Similarity	NPD4747	Approved
0.8451	Intermediate Similarity	NPD4691	Approved
0.8101	Intermediate Similarity	NPD3527	Clinical (unspecified phase)
0.7917	Intermediate Similarity	NPD3621	Clinical (unspecified phase)
0.7831	Intermediate Similarity	NPD4518	Approved
0.759	Intermediate Similarity	NPD5280	Approved
0.759	Intermediate Similarity	NPD4694	Approved
0.759	Intermediate Similarity	NPD5279	Phase 3
0.7442	Intermediate Similarity	NPD5207	Approved
0.7381	Intermediate Similarity	NPD5690	Phase 2
0.7356	Intermediate Similarity	NPD5281	Approved
0.7356	Intermediate Similarity	NPD5694	Approved
0.7356	Intermediate Similarity	NPD6050	Approved
0.7356	Intermediate Similarity	NPD5284	Approved
0.7317	Intermediate Similarity	NPD4223	Phase 3
0.7317	Intermediate Similarity	NPD4221	Approved
0.7262	Intermediate Similarity	NPD5329	Approved
0.7241	Intermediate Similarity	NPD5692	Phase 3
0.7241	Intermediate Similarity	NPD4096	Approved
0.7176	Intermediate Similarity	NPD6409	Approved
0.7176	Intermediate Similarity	NPD6684	Approved
0.7176	Intermediate Similarity	NPD5330	Approved
0.7176	Intermediate Similarity	NPD7334	Approved
0.7176	Intermediate Similarity	NPD7521	Approved
0.7176	Intermediate Similarity	NPD7146	Approved
0.7143	Intermediate Similarity	NPD3665	Phase 1
0.7143	Intermediate Similarity	NPD3666	Approved
0.7143	Intermediate Similarity	NPD3133	Approved
0.7143	Intermediate Similarity	NPD287	Approved
0.7143	Intermediate Similarity	NPD4197	Approved
0.7073	Intermediate Similarity	NPD8259	Clinical (unspecified phase)
0.7037	Intermediate Similarity	NPD3617	Approved
0.7011	Intermediate Similarity	NPD5737	Approved
0.7011	Intermediate Similarity	NPD6903	Approved
0.7011	Intermediate Similarity	NPD7513	Clinical (unspecified phase)
0.7011	Intermediate Similarity	NPD6672	Approved
0.6988	Remote Similarity	NPD8028	Phase 2
0.6977	Remote Similarity	NPD4138	Approved
0.6977	Remote Similarity	NPD5205	Approved
0.6977	Remote Similarity	NPD4693	Phase 3
0.6977	Remote Similarity	NPD4688	Approved
0.6977	Remote Similarity	NPD4690	Approved
0.6977	Remote Similarity	NPD3618	Phase 1
0.6977	Remote Similarity	NPD4689	Approved
0.6966	Remote Similarity	NPD6079	Approved
0.6941	Remote Similarity	NPD4786	Approved
0.6932	Remote Similarity	NPD5328	Approved
0.6932	Remote Similarity	NPD6673	Approved
0.6932	Remote Similarity	NPD6904	Approved
0.6932	Remote Similarity	NPD6080	Approved
0.6905	Remote Similarity	NPD3667	Approved
0.6889	Remote Similarity	NPD5133	Approved
0.6867	Remote Similarity	NPD4695	Discontinued
0.6818	Remote Similarity	NPD5208	Approved
0.6782	Remote Similarity	NPD6098	Approved
0.6782	Remote Similarity	NPD4623	Approved
0.6782	Remote Similarity	NPD4519	Discontinued
0.6782	Remote Similarity	NPD3574	Clinical (unspecified phase)
0.6747	Remote Similarity	NPD4195	Approved
0.6744	Remote Similarity	NPD3668	Phase 3
0.6742	Remote Similarity	NPD4753	Phase 2
0.6742	Remote Similarity	NPD7285	Clinical (unspecified phase)
0.6739	Remote Similarity	NPD5654	Approved
0.6711	Remote Similarity	NPD7331	Phase 2
0.6622	Remote Similarity	NPD4191	Approved
0.6622	Remote Similarity	NPD4194	Approved
0.6622	Remote Similarity	NPD4192	Approved
0.6622	Remote Similarity	NPD4193	Approved
0.6596	Remote Similarity	NPD5959	Approved
0.6593	Remote Similarity	NPD5693	Phase 1
0.6588	Remote Similarity	NPD4692	Approved
0.6588	Remote Similarity	NPD4139	Approved
0.6567	Remote Similarity	NPD8262	Approved
0.6559	Remote Similarity	NPD5210	Approved
0.6559	Remote Similarity	NPD5695	Phase 3
0.6559	Remote Similarity	NPD6356	Clinical (unspecified phase)
0.6559	Remote Similarity	NPD4629	Approved
0.6522	Remote Similarity	NPD4202	Approved
0.6517	Remote Similarity	NPD3573	Approved
0.6489	Remote Similarity	NPD5222	Approved
0.6489	Remote Similarity	NPD5221	Approved
0.6489	Remote Similarity	NPD5220	Clinical (unspecified phase)
0.6463	Remote Similarity	NPD8039	Approved
0.6458	Remote Similarity	NPD6404	Discontinued
0.6452	Remote Similarity	NPD6001	Approved
0.6429	Remote Similarity	NPD5784	Clinical (unspecified phase)
0.6421	Remote Similarity	NPD6084	Phase 2
0.6421	Remote Similarity	NPD5173	Approved
0.6421	Remote Similarity	NPD6083	Phase 2
0.6413	Remote Similarity	NPD6411	Approved
0.6375	Remote Similarity	NPD7144	Approved
0.6375	Remote Similarity	NPD7143	Approved
0.6364	Remote Similarity	NPD7341	Phase 2
0.6344	Remote Similarity	NPD6399	Phase 3
0.6316	Remote Similarity	NPD4697	Phase 3
0.6296	Remote Similarity	NPD7152	Approved
0.6296	Remote Similarity	NPD7150	Approved
0.6296	Remote Similarity	NPD7151	Approved
0.6289	Remote Similarity	NPD5286	Approved
0.6289	Remote Similarity	NPD4696	Approved
0.6289	Remote Similarity	NPD5285	Approved
0.625	Remote Similarity	NPD6923	Approved
0.625	Remote Similarity	NPD6922	Approved
0.625	Remote Similarity	NPD3495	Discontinued
0.625	Remote Similarity	NPD4755	Approved
0.625	Remote Similarity	NPD4788	Approved
0.6237	Remote Similarity	NPD7515	Phase 2
0.6234	Remote Similarity	NPD5325	Clinical (unspecified phase)
0.6224	Remote Similarity	NPD5223	Approved
0.6196	Remote Similarity	NPD5764	Clinical (unspecified phase)
0.6196	Remote Similarity	NPD6101	Approved
0.6186	Remote Similarity	NPD5696	Approved
0.617	Remote Similarity	NPD7631	Approved
0.6162	Remote Similarity	NPD5226	Approved
0.6162	Remote Similarity	NPD4633	Approved
0.6162	Remote Similarity	NPD5211	Phase 2
0.6162	Remote Similarity	NPD5225	Approved
0.6162	Remote Similarity	NPD5091	Approved
0.6162	Remote Similarity	NPD5224	Approved
0.6145	Remote Similarity	NPD6926	Approved
0.6145	Remote Similarity	NPD6924	Approved
0.6145	Remote Similarity	NPD4784	Approved
0.6145	Remote Similarity	NPD4785	Approved
0.6136	Remote Similarity	NPD4752	Clinical (unspecified phase)
0.6122	Remote Similarity	NPD4700	Approved
0.6118	Remote Similarity	NPD6932	Approved
0.6111	Remote Similarity	NPD1694	Approved
0.6105	Remote Similarity	NPD7901	Clinical (unspecified phase)
0.6105	Remote Similarity	NPD7748	Approved
0.6105	Remote Similarity	NPD7900	Approved
0.61	Remote Similarity	NPD6052	Approved
0.61	Remote Similarity	NPD5174	Approved
0.61	Remote Similarity	NPD5175	Approved
0.6098	Remote Similarity	NPD4243	Approved
0.6078	Remote Similarity	NPD6614	Approved
0.6076	Remote Similarity	NPD6108	Clinical (unspecified phase)
0.6071	Remote Similarity	NPD8264	Approved
0.6064	Remote Similarity	NPD7609	Phase 3
0.6047	Remote Similarity	NPD7145	Approved
0.604	Remote Similarity	NPD5141	Approved
0.6038	Remote Similarity	NPD6858	Approved
0.6038	Remote Similarity	NPD7094	Approved
0.6019	Remote Similarity	NPD6881	Approved
0.6019	Remote Similarity	NPD6899	Approved
0.6	Remote Similarity	NPD6933	Approved
0.598	Remote Similarity	NPD7128	Approved
0.598	Remote Similarity	NPD6402	Approved
0.598	Remote Similarity	NPD5739	Approved
0.598	Remote Similarity	NPD6675	Approved
0.5979	Remote Similarity	NPD7732	Phase 3
0.5979	Remote Similarity	NPD7614	Phase 1
0.5957	Remote Similarity	NPD5785	Approved
0.5955	Remote Similarity	NPD5209	Approved
0.5946	Remote Similarity	NPD4219	Approved
0.5941	Remote Similarity	NPD4754	Approved
0.5938	Remote Similarity	NPD5769	Clinical (unspecified phase)
0.5934	Remote Similarity	NPD5363	Approved
0.593	Remote Similarity	NPD6925	Approved
0.593	Remote Similarity	NPD5776	Phase 2
0.5922	Remote Similarity	NPD5697	Approved
0.5922	Remote Similarity	NPD6412	Phase 2
0.5918	Remote Similarity	NPD7902	Approved
0.5909	Remote Similarity	NPD5368	Approved
0.5909	Remote Similarity	NPD7514	Phase 3
0.5905	Remote Similarity	NPD6883	Approved
0.5905	Remote Similarity	NPD7102	Approved
0.5905	Remote Similarity	NPD7290	Approved
0.5895	Remote Similarity	NPD7637	Suspended
0.5882	Remote Similarity	NPD6942	Approved
0.5882	Remote Similarity	NPD7339	Approved
0.5865	Remote Similarity	NPD7320	Approved
0.5865	Remote Similarity	NPD5168	Approved
0.5865	Remote Similarity	NPD6011	Approved
0.5865	Remote Similarity	NPD4730	Approved
0.5865	Remote Similarity	NPD4729	Approved
0.5862	Remote Similarity	NPD7322	Clinical (unspecified phase)
0.5849	Remote Similarity	NPD6617	Approved
0.5849	Remote Similarity	NPD6847	Approved
0.5849	Remote Similarity	NPD6649	Approved
0.5849	Remote Similarity	NPD6869	Approved
0.5849	Remote Similarity	NPD6650	Approved
0.5849	Remote Similarity	NPD8130	Phase 1
0.5843	Remote Similarity	NPD6902	Approved
0.5843	Remote Similarity	NPD5369	Approved
0.5833	Remote Similarity	NPD5779	Approved
0.5833	Remote Similarity	NPD5778	Approved
0.5833	Remote Similarity	NPD1508	Approved
0.5825	Remote Similarity	NPD4767	Approved
0.5825	Remote Similarity	NPD6008	Approved
0.5825	Remote Similarity	NPD4768	Approved
0.5814	Remote Similarity	NPD3701	Clinical (unspecified phase)
0.5811	Remote Similarity	NPD4627	Clinical (unspecified phase)
0.581	Remote Similarity	NPD6012	Approved
0.581	Remote Similarity	NPD6372	Approved
0.581	Remote Similarity	NPD6014	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