NPASS Compound

Structure

CID20853 OpenBabel06191715342D 32 36 0 0 1 0 0 0 0 0999 V2000 -2.6652 2.9240 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2037 3.7683 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2314 -1.4630 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7274 -0.5901 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6667 -1.9642 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8456 2.4652 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8451 -0.4882 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0002 0.9751 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5344 0.4879 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3789 0.0008 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8454 -1.4634 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3792 -2.9254 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5348 -2.4379 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0002 -0.9763 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0005 1.9502 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8447 1.4632 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5343 1.4624 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6908 2.9243 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6903 -0.9759 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6901 0.0004 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6905 1.9498 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.5340 0.4867 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.3792 -0.9755 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.2235 -2.4379 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8451 0.4871 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.2235 -1.4630 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5348 -1.4630 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8454 1.4628 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8449 0.4875 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 -3.2410 -0.2206 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.0963 -2.9418 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 18 1 0 0 0 0 2 18 1 0 0 0 0 3 26 1 0 0 0 0 4 26 1 0 0 0 0 7 29 1 0 0 0 0 9 10 1 0 0 0 0 9 20 2 0 0 0 0 10 23 1 0 0 0 0 11 14 1 0 0 0 0 11 19 2 0 0 0 0 12 13 1 0 0 0 0 12 24 1 0 0 0 0 13 27 1 0 0 0 0 14 30 1 0 0 0 0 15 16 1 0 0 0 0 15 28 1 0 0 0 0 16 29 1 0 0 0 0 17 21 1 0 0 0 0 17 22 1 0 0 0 0 18 21 1 0 0 0 0 19 20 1 0 0 0 0 19 27 1 0 0 0 0 20 29 1 0 0 0 0 21 28 1 1 0 0 0 22 25 1 0 0 0 0 22 31 1 6 0 0 0 23 26 1 0 0 0 0 23 27 1 1 0 0 0 24 26 1 0 0 0 0 24 32 1 1 0 0 0 25 28 1 1 0 0 0 25 30 1 0 0 0 0 27 5 1 1 0 0 0 28 6 1 1 0 0 0 29 30 1 1 0 0 0 30 8 1 1 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	546.15
Volume:	544.202
LogP:	4.357
LogD:	2.637
LogS:	-3.299
# Rotatable Bonds:	7
TPSA:	181.8
# H-Bond Aceptor:	10
# H-Bond Donor:	6
# Rings:	4
# Heavy Atoms:	10

MedChem Properties

QED Drug-Likeness Score:	0.173
Synthetic Accessibility Score:	3.404
Fsp3:	0.133
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Rejected
Chelating Alert:	1
PAINS Alert:	1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.658
MDCK Permeability:	1.2235095709911548e-05
Pgp-inhibitor:	0.026
Pgp-substrate:	0.958
Human Intestinal Absorption (HIA):	0.089
20% Bioavailability (F20%):	0.32
30% Bioavailability (F30%):	0.992

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.002
Plasma Protein Binding (PPB):	100.00607299804688%
Volume Distribution (VD):	0.155
Pgp-substrate:	0.9310187101364136%

ADMET: Metabolism

CYP1A2-inhibitor:	0.266
CYP1A2-substrate:	0.877
CYP2C19-inhibitor:	0.175
CYP2C19-substrate:	0.046
CYP2C9-inhibitor:	0.757
CYP2C9-substrate:	0.911
CYP2D6-inhibitor:	0.045
CYP2D6-substrate:	0.872
CYP3A4-inhibitor:	0.114
CYP3A4-substrate:	0.168

ADMET: Excretion

Clearance (CL):	5.989
Half-life (T1/2):	0.745

ADMET: Toxicity

hERG Blockers:	0.143
Human Hepatotoxicity (H-HT):	0.738
Drug-inuced Liver Injury (DILI):	0.98
AMES Toxicity:	0.008
Rat Oral Acute Toxicity:	0.164
Maximum Recommended Daily Dose:	0.904
Skin Sensitization:	0.969
Carcinogencity:	0.131
Eye Corrosion:	0.003
Eye Irritation:	0.659
Respiratory Toxicity:	0.036

Download Data

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

Natural Product: NPC20853

Natural Product ID:	NPC20853
*Common Name:**	Rubiyunnanol A
IUPAC Name:	(1R,3S,3aS,5aR,7aR,9S,11aS,13aR,13bS)-3a,5a,8,8,11a,13a-hexamethyl-3-propan-2-yl-1,2,3,4,5,7,7a,9,10,11,13,13b-dodecahydrocyclopenta[a]chrysene-1,9-diol
Synonyms:	rubiyunnanol A
Standard InCHIKey:	VGCPCEYHYXKGCA-ZMTMDZEFSA-N
Standard InCHI:	InChI=1S/C30H48O2/c1-18(2)21-17-22(31)25-28(21,6)15-16-29(7)20-9-10-23-26(3,4)24(32)12-13-27(23,5)19(20)11-14-30(25,29)8/h9,11,18,21-25,31-32H,10,12-17H2,1-8H3/t21-,22+,23-,24-,25-,27+,28-,29-,30+/m0/s1
SMILES:	CC(C)[C@@H]1C[C@H]([C@H]2[C@@]1(C)CC[C@@]1(C)C3=CC[C@H]4C(C)(C)[C@H](CC[C@]4(C)C3=CC[C@]21C)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL1835872
PubChem CID:	56599863
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001553] Triterpenoids

*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
NPO16607	Rubia yunnanensis	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12350148]
NPO16607	Rubia yunnanensis	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12762798]
NPO16607	Rubia yunnanensis	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21044847]
NPO16607	Rubia yunnanensis	Species	Rubiaceae	Eukaryota	roots	n.a.	n.a.	PMID[21973054]
NPO16607	Rubia yunnanensis	Species	Rubiaceae	Eukaryota	n.a.	root	n.a.	PMID[21973054]
NPO16607	Rubia yunnanensis	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO16607	Rubia yunnanensis	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO16607	Rubia yunnanensis	Species	Rubiaceae	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	2

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT81	Cell Line	A549	Homo sapiens	IC50	=	9800.0	nM	PMID[518073]
NPT165	Cell Line	HeLa	Homo sapiens	IC50	>	10000.0	nM	PMID[518073]

☑ 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 NPC20853 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	163
0.1-0.2	1413
0.2-0.3	7031
0.3-0.4	16646
0.4-0.5	6986
0.5-0.6	5534
0.6-0.7	3652
0.7-0.8	1044
0.8-0.85	153
0.85-0.9	69
0.9-0.95	5
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
0.9487	High Similarity	NPC201852
0.9351	High Similarity	NPC1319
0.9268	High Similarity	NPC470542
0.9221	High Similarity	NPC205455
0.9221	High Similarity	NPC186191
0.9114	High Similarity	NPC6707
0.9091	High Similarity	NPC214570
0.9012	High Similarity	NPC209802
0.9	High Similarity	NPC202389
0.8974	High Similarity	NPC72507
0.8974	High Similarity	NPC318136
0.8974	High Similarity	NPC477522
0.8974	High Similarity	NPC275910
0.8961	High Similarity	NPC202642
0.8961	High Similarity	NPC46160
0.8961	High Similarity	NPC189883
0.8961	High Similarity	NPC73875
0.8916	High Similarity	NPC271967
0.8831	High Similarity	NPC141071
0.8831	High Similarity	NPC322353
0.8831	High Similarity	NPC471723
0.8831	High Similarity	NPC118508
0.8831	High Similarity	NPC121744
0.8831	High Similarity	NPC257347
0.8816	High Similarity	NPC201373
0.881	High Similarity	NPC2158
0.8795	High Similarity	NPC24277
0.878	High Similarity	NPC231310
0.878	High Similarity	NPC124172
0.875	High Similarity	NPC26117
0.875	High Similarity	NPC236112
0.8734	High Similarity	NPC307965
0.8734	High Similarity	NPC477514
0.8734	High Similarity	NPC167037
0.8734	High Similarity	NPC285761
0.8734	High Similarity	NPC18603
0.8734	High Similarity	NPC76931
0.8734	High Similarity	NPC244385
0.8734	High Similarity	NPC6978
0.8734	High Similarity	NPC138621
0.8718	High Similarity	NPC300324
0.8718	High Similarity	NPC96319
0.8718	High Similarity	NPC106432
0.8718	High Similarity	NPC321016
0.8718	High Similarity	NPC321381
0.8718	High Similarity	NPC240604
0.8718	High Similarity	NPC237460
0.8718	High Similarity	NPC134330
0.8718	High Similarity	NPC107059
0.8718	High Similarity	NPC129165
0.8718	High Similarity	NPC470362
0.8675	High Similarity	NPC318390
0.8659	High Similarity	NPC477818
0.8659	High Similarity	NPC110778
0.8642	High Similarity	NPC474531
0.8625	High Similarity	NPC30986
0.8625	High Similarity	NPC80530
0.8625	High Similarity	NPC209430
0.8625	High Similarity	NPC273410
0.8608	High Similarity	NPC155986
0.8608	High Similarity	NPC198968
0.8608	High Similarity	NPC318495
0.8605	High Similarity	NPC107189
0.859	High Similarity	NPC285893
0.859	High Similarity	NPC304309
0.859	High Similarity	NPC230301
0.859	High Similarity	NPC162742
0.859	High Similarity	NPC134847
0.859	High Similarity	NPC288035
0.859	High Similarity	NPC22105
0.859	High Similarity	NPC28657
0.859	High Similarity	NPC136188
0.8554	High Similarity	NPC238485
0.8537	High Similarity	NPC1272
0.8537	High Similarity	NPC30166
0.8537	High Similarity	NPC248886
0.8537	High Similarity	NPC87489
0.8537	High Similarity	NPC470049
0.8537	High Similarity	NPC470614
0.8519	High Similarity	NPC102253
0.8519	High Similarity	NPC236237
0.8519	High Similarity	NPC322313
0.8519	High Similarity	NPC13554
0.85	High Similarity	NPC474216
0.85	High Similarity	NPC42853
0.85	High Similarity	NPC87604
0.85	High Similarity	NPC302041
0.85	High Similarity	NPC473943
0.85	High Similarity	NPC85346
0.85	High Similarity	NPC65897
0.8488	Intermediate Similarity	NPC105495
0.8481	Intermediate Similarity	NPC113733
0.8471	Intermediate Similarity	NPC475772
0.8462	Intermediate Similarity	NPC100334
0.8442	Intermediate Similarity	NPC110799
0.8434	Intermediate Similarity	NPC237795
0.8434	Intermediate Similarity	NPC82538
0.8434	Intermediate Similarity	NPC470384
0.8434	Intermediate Similarity	NPC193870
0.8434	Intermediate Similarity	NPC141941
0.8415	Intermediate Similarity	NPC470383
0.8395	Intermediate Similarity	NPC84694
0.8395	Intermediate Similarity	NPC49599
0.8395	Intermediate Similarity	NPC49627
0.8395	Intermediate Similarity	NPC143182
0.8395	Intermediate Similarity	NPC328714
0.8395	Intermediate Similarity	NPC109546
0.8395	Intermediate Similarity	NPC28862
0.8395	Intermediate Similarity	NPC47982
0.8395	Intermediate Similarity	NPC81306
0.8375	Intermediate Similarity	NPC40394
0.8375	Intermediate Similarity	NPC157996
0.8375	Intermediate Similarity	NPC34019
0.8375	Intermediate Similarity	NPC101475
0.8375	Intermediate Similarity	NPC34177
0.8375	Intermediate Similarity	NPC472805
0.8375	Intermediate Similarity	NPC90979
0.8372	Intermediate Similarity	NPC280556
0.8354	Intermediate Similarity	NPC231256
0.8354	Intermediate Similarity	NPC138374
0.8354	Intermediate Similarity	NPC34700
0.8354	Intermediate Similarity	NPC104387
0.8354	Intermediate Similarity	NPC240235
0.8354	Intermediate Similarity	NPC471468
0.8354	Intermediate Similarity	NPC178383
0.8354	Intermediate Similarity	NPC212879
0.8353	Intermediate Similarity	NPC201273
0.8333	Intermediate Similarity	NPC474140
0.8333	Intermediate Similarity	NPC478102
0.8333	Intermediate Similarity	NPC470077
0.8333	Intermediate Similarity	NPC474493
0.8333	Intermediate Similarity	NPC475798
0.8333	Intermediate Similarity	NPC127606
0.8333	Intermediate Similarity	NPC182717
0.8313	Intermediate Similarity	NPC49964
0.8313	Intermediate Similarity	NPC218616
0.8313	Intermediate Similarity	NPC101462
0.8313	Intermediate Similarity	NPC296701
0.8313	Intermediate Similarity	NPC5985
0.8293	Intermediate Similarity	NPC22403
0.8293	Intermediate Similarity	NPC241290
0.8293	Intermediate Similarity	NPC234193
0.8293	Intermediate Similarity	NPC164840
0.8293	Intermediate Similarity	NPC209944
0.8276	Intermediate Similarity	NPC84271
0.8276	Intermediate Similarity	NPC102414
0.8276	Intermediate Similarity	NPC77168
0.8272	Intermediate Similarity	NPC253807
0.8272	Intermediate Similarity	NPC230295
0.8272	Intermediate Similarity	NPC22955
0.8272	Intermediate Similarity	NPC477819
0.8272	Intermediate Similarity	NPC196753
0.8272	Intermediate Similarity	NPC474989
0.8272	Intermediate Similarity	NPC477817
0.8272	Intermediate Similarity	NPC312328
0.8272	Intermediate Similarity	NPC158662
0.8272	Intermediate Similarity	NPC300499
0.8272	Intermediate Similarity	NPC98386
0.8272	Intermediate Similarity	NPC470396
0.8272	Intermediate Similarity	NPC99168
0.825	Intermediate Similarity	NPC14112
0.825	Intermediate Similarity	NPC290598
0.825	Intermediate Similarity	NPC30590
0.825	Intermediate Similarity	NPC93662
0.825	Intermediate Similarity	NPC122418
0.825	Intermediate Similarity	NPC120098
0.825	Intermediate Similarity	NPC265328
0.825	Intermediate Similarity	NPC244488
0.825	Intermediate Similarity	NPC278091
0.825	Intermediate Similarity	NPC86305
0.825	Intermediate Similarity	NPC78067
0.825	Intermediate Similarity	NPC247325
0.825	Intermediate Similarity	NPC27765
0.8235	Intermediate Similarity	NPC474349
0.8235	Intermediate Similarity	NPC474189
0.8228	Intermediate Similarity	NPC62657
0.8228	Intermediate Similarity	NPC192638
0.8228	Intermediate Similarity	NPC477138
0.8228	Intermediate Similarity	NPC469593
0.8228	Intermediate Similarity	NPC243342
0.8228	Intermediate Similarity	NPC25511
0.8228	Intermediate Similarity	NPC469534
0.8228	Intermediate Similarity	NPC329090
0.8228	Intermediate Similarity	NPC469533
0.8228	Intermediate Similarity	NPC27395
0.8228	Intermediate Similarity	NPC91858
0.8222	Intermediate Similarity	NPC162001
0.8222	Intermediate Similarity	NPC222845
0.8222	Intermediate Similarity	NPC45324
0.8214	Intermediate Similarity	NPC113978
0.8214	Intermediate Similarity	NPC207013
0.8214	Intermediate Similarity	NPC317458
0.8205	Intermediate Similarity	NPC167706
0.8205	Intermediate Similarity	NPC111234
0.8193	Intermediate Similarity	NPC474759
0.8193	Intermediate Similarity	NPC47761
0.8193	Intermediate Similarity	NPC82986
0.8193	Intermediate Similarity	NPC7505
0.8193	Intermediate Similarity	NPC264245
0.8193	Intermediate Similarity	NPC474752

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 NPC20853 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	161
0.1-0.2	1597
0.2-0.3	4509
0.3-0.4	2066
0.4-0.5	402
0.5-0.6	140
0.6-0.7	168
0.7-0.8	91
0.8-0.85	13
0.85-0.9	3
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8718	High Similarity	NPD3701	Clinical (unspecified phase)
0.859	High Similarity	NPD6942	Approved
0.859	High Similarity	NPD7339	Approved
0.8519	High Similarity	NPD7525	Registered
0.8293	Intermediate Similarity	NPD4748	Discontinued
0.8228	Intermediate Similarity	NPD6926	Approved
0.8228	Intermediate Similarity	NPD6924	Approved
0.8205	Intermediate Similarity	NPD4243	Approved
0.8171	Intermediate Similarity	NPD7645	Phase 2
0.8025	Intermediate Similarity	NPD6933	Approved
0.8	Intermediate Similarity	NPD4785	Approved
0.8	Intermediate Similarity	NPD4784	Approved
0.7975	Intermediate Similarity	NPD7150	Approved
0.7975	Intermediate Similarity	NPD7152	Approved
0.7975	Intermediate Similarity	NPD7151	Approved
0.7949	Intermediate Similarity	NPD6923	Approved
0.7949	Intermediate Similarity	NPD6922	Approved
0.7907	Intermediate Similarity	NPD4786	Approved
0.7865	Intermediate Similarity	NPD5328	Approved
0.7848	Intermediate Similarity	NPD7143	Approved
0.7848	Intermediate Similarity	NPD7144	Approved
0.7841	Intermediate Similarity	NPD4751	Clinical (unspecified phase)
0.7802	Intermediate Similarity	NPD4202	Approved
0.7738	Intermediate Similarity	NPD6929	Approved
0.7727	Intermediate Similarity	NPD3618	Phase 1
0.7701	Intermediate Similarity	NPD3665	Phase 1
0.7701	Intermediate Similarity	NPD3133	Approved
0.7701	Intermediate Similarity	NPD3666	Approved
0.7692	Intermediate Similarity	NPD6079	Approved
0.7683	Intermediate Similarity	NPD4190	Phase 3
0.7683	Intermediate Similarity	NPD5275	Approved
0.7674	Intermediate Similarity	NPD3667	Approved
0.7647	Intermediate Similarity	NPD6930	Phase 2
0.7647	Intermediate Similarity	NPD7509	Discontinued
0.7647	Intermediate Similarity	NPD6931	Approved
0.7529	Intermediate Similarity	NPD4195	Approved
0.7528	Intermediate Similarity	NPD5279	Phase 3
0.75	Intermediate Similarity	NPD6925	Approved
0.75	Intermediate Similarity	NPD6932	Approved
0.75	Intermediate Similarity	NPD5776	Phase 2
0.7474	Intermediate Similarity	NPD4755	Approved
0.747	Intermediate Similarity	NPD8264	Approved
0.7416	Intermediate Similarity	NPD7520	Clinical (unspecified phase)
0.7412	Intermediate Similarity	NPD7145	Approved
0.7386	Intermediate Similarity	NPD6695	Phase 3
0.7333	Intermediate Similarity	NPD4694	Approved
0.7333	Intermediate Similarity	NPD5280	Approved
0.7326	Intermediate Similarity	NPD6683	Phase 2
0.732	Intermediate Similarity	NPD4700	Approved
0.732	Intermediate Similarity	NPD5285	Approved
0.732	Intermediate Similarity	NPD5286	Approved
0.732	Intermediate Similarity	NPD4696	Approved
0.7303	Intermediate Similarity	NPD7338	Clinical (unspecified phase)
0.7283	Intermediate Similarity	NPD4753	Phase 2
0.7273	Intermediate Similarity	NPD4221	Approved
0.7273	Intermediate Similarity	NPD4223	Phase 3
0.7245	Intermediate Similarity	NPD5223	Approved
0.7241	Intermediate Similarity	NPD7514	Phase 3
0.7222	Intermediate Similarity	NPD5329	Approved
0.7222	Intermediate Similarity	NPD6893	Approved
0.7209	Intermediate Similarity	NPD7322	Clinical (unspecified phase)
0.7195	Intermediate Similarity	NPD4787	Phase 1
0.7188	Intermediate Similarity	NPD4697	Phase 3
0.7188	Intermediate Similarity	NPD5220	Clinical (unspecified phase)
0.7188	Intermediate Similarity	NPD5221	Approved
0.7188	Intermediate Similarity	NPD5222	Approved
0.7172	Intermediate Similarity	NPD5211	Phase 2
0.7172	Intermediate Similarity	NPD4633	Approved
0.7172	Intermediate Similarity	NPD5225	Approved
0.7172	Intermediate Similarity	NPD5226	Approved
0.7172	Intermediate Similarity	NPD5224	Approved
0.7159	Intermediate Similarity	NPD6902	Approved
0.7129	Intermediate Similarity	NPD5739	Approved
0.7129	Intermediate Similarity	NPD6675	Approved
0.7129	Intermediate Similarity	NPD6402	Approved
0.7129	Intermediate Similarity	NPD7128	Approved
0.7128	Intermediate Similarity	NPD7515	Phase 2
0.7113	Intermediate Similarity	NPD5173	Approved
0.7111	Intermediate Similarity	NPD4197	Approved
0.71	Intermediate Similarity	NPD5175	Approved
0.71	Intermediate Similarity	NPD5174	Approved
0.71	Intermediate Similarity	NPD4754	Approved
0.7073	Intermediate Similarity	NPD4267	Clinical (unspecified phase)
0.7065	Intermediate Similarity	NPD7524	Approved
0.7065	Intermediate Similarity	NPD7750	Discontinued
0.7053	Intermediate Similarity	NPD6399	Phase 3
0.7045	Intermediate Similarity	NPD7332	Phase 2
0.7041	Intermediate Similarity	NPD7638	Approved
0.703	Intermediate Similarity	NPD5141	Approved
0.7	Intermediate Similarity	NPD4788	Approved
0.699	Remote Similarity	NPD6881	Approved
0.699	Remote Similarity	NPD7320	Approved
0.699	Remote Similarity	NPD6899	Approved
0.6989	Remote Similarity	NPD7513	Clinical (unspecified phase)
0.697	Remote Similarity	NPD7639	Approved
0.697	Remote Similarity	NPD7640	Approved
0.6966	Remote Similarity	NPD6898	Phase 1
0.6966	Remote Similarity	NPD4692	Approved
0.6966	Remote Similarity	NPD4139	Approved
0.6961	Remote Similarity	NPD4768	Approved
0.6961	Remote Similarity	NPD4767	Approved
0.6957	Remote Similarity	NPD4690	Approved
0.6957	Remote Similarity	NPD4688	Approved
0.6957	Remote Similarity	NPD4689	Approved
0.6957	Remote Similarity	NPD6409	Approved
0.6957	Remote Similarity	NPD7146	Approved
0.6957	Remote Similarity	NPD4693	Phase 3
0.6957	Remote Similarity	NPD7521	Approved
0.6957	Remote Similarity	NPD5330	Approved
0.6957	Remote Similarity	NPD4138	Approved
0.6957	Remote Similarity	NPD6684	Approved
0.6957	Remote Similarity	NPD3574	Clinical (unspecified phase)
0.6957	Remote Similarity	NPD5690	Phase 2
0.6957	Remote Similarity	NPD5205	Approved
0.6957	Remote Similarity	NPD7334	Approved
0.6947	Remote Similarity	NPD5281	Approved
0.6947	Remote Similarity	NPD5284	Approved
0.6939	Remote Similarity	NPD6084	Phase 2
0.6939	Remote Similarity	NPD6083	Phase 2
0.6923	Remote Similarity	NPD6372	Approved
0.6923	Remote Similarity	NPD3668	Phase 3
0.6923	Remote Similarity	NPD6373	Approved
0.6915	Remote Similarity	NPD6051	Approved
0.6907	Remote Similarity	NPD5210	Approved
0.6907	Remote Similarity	NPD4629	Approved
0.6893	Remote Similarity	NPD5701	Approved
0.6893	Remote Similarity	NPD5697	Approved
0.6875	Remote Similarity	NPD5133	Approved
0.6869	Remote Similarity	NPD5290	Discontinued
0.6857	Remote Similarity	NPD6883	Approved
0.6857	Remote Similarity	NPD7290	Approved
0.6857	Remote Similarity	NPD7102	Approved
0.6842	Remote Similarity	NPD4096	Approved
0.6827	Remote Similarity	NPD6011	Approved
0.6827	Remote Similarity	NPD5128	Approved
0.6827	Remote Similarity	NPD4729	Approved
0.6827	Remote Similarity	NPD4730	Approved
0.6809	Remote Similarity	NPD6903	Approved
0.6809	Remote Similarity	NPD4723	Approved
0.6809	Remote Similarity	NPD4722	Approved
0.6804	Remote Similarity	NPD7748	Approved
0.6792	Remote Similarity	NPD6650	Approved
0.6792	Remote Similarity	NPD6617	Approved
0.6792	Remote Similarity	NPD6869	Approved
0.6792	Remote Similarity	NPD8130	Phase 1
0.6792	Remote Similarity	NPD6649	Approved
0.6792	Remote Similarity	NPD6401	Clinical (unspecified phase)
0.6792	Remote Similarity	NPD6847	Approved
0.6771	Remote Similarity	NPD8035	Phase 2
0.6771	Remote Similarity	NPD8034	Phase 2
0.6771	Remote Similarity	NPD7087	Discontinued
0.6762	Remote Similarity	NPD6013	Approved
0.6762	Remote Similarity	NPD6014	Approved
0.6762	Remote Similarity	NPD6012	Approved
0.6735	Remote Similarity	NPD5695	Phase 3
0.6733	Remote Similarity	NPD4159	Approved
0.6729	Remote Similarity	NPD6882	Approved
0.6729	Remote Similarity	NPD8297	Approved
0.6706	Remote Similarity	NPD4808	Clinical (unspecified phase)
0.6706	Remote Similarity	NPD4809	Clinical (unspecified phase)
0.6698	Remote Similarity	NPD5251	Approved
0.6698	Remote Similarity	NPD5248	Approved
0.6698	Remote Similarity	NPD5249	Phase 3
0.6698	Remote Similarity	NPD4634	Approved
0.6698	Remote Similarity	NPD5247	Approved
0.6698	Remote Similarity	NPD5250	Approved
0.6698	Remote Similarity	NPD5134	Clinical (unspecified phase)
0.6698	Remote Similarity	NPD5135	Approved
0.6698	Remote Similarity	NPD5169	Approved
0.6667	Remote Similarity	NPD6928	Phase 2
0.6636	Remote Similarity	NPD5216	Approved
0.6636	Remote Similarity	NPD5217	Approved
0.6636	Remote Similarity	NPD5215	Approved
0.6636	Remote Similarity	NPD5127	Approved
0.6632	Remote Similarity	NPD4518	Approved
0.6629	Remote Similarity	NPD3617	Approved
0.66	Remote Similarity	NPD7902	Approved
0.6598	Remote Similarity	NPD6050	Approved
0.6596	Remote Similarity	NPD6098	Approved
0.6591	Remote Similarity	NPD6117	Approved
0.6588	Remote Similarity	NPD4245	Approved
0.6588	Remote Similarity	NPD4244	Approved
0.6571	Remote Similarity	NPD6412	Phase 2
0.6566	Remote Similarity	NPD6356	Clinical (unspecified phase)
0.6562	Remote Similarity	NPD7285	Clinical (unspecified phase)
0.6552	Remote Similarity	NPD6113	Clinical (unspecified phase)
0.6552	Remote Similarity	NPD5733	Approved
0.6549	Remote Similarity	NPD7503	Approved
0.6535	Remote Similarity	NPD5696	Approved
0.6517	Remote Similarity	NPD6116	Phase 1
0.6514	Remote Similarity	NPD4632	Approved
0.6509	Remote Similarity	NPD5168	Approved
0.6505	Remote Similarity	NPD7632	Discontinued
0.6495	Remote Similarity	NPD5207	Approved
0.6495	Remote Similarity	NPD5692	Phase 3
0.6495	Remote Similarity	NPD4001	Clinical (unspecified phase)
0.6471	Remote Similarity	NPD3698	Phase 2
0.6471	Remote Similarity	NPD3699	Clinical (unspecified phase)
0.6471	Remote Similarity	NPD3700	Clinical (unspecified phase)
0.6458	Remote Similarity	NPD5737	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