NPASS Compound

Structure

CID3629 OpenBabel06191715322D 34 37 0 0 1 0 0 0 0 0999 V2000 -4.3301 -4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 -6.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -6.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3660 1.3660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3660 1.3660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -5.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -6.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -6.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -4.5000 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 0.0000 -4.0000 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 -3.4641 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -5.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -5.5000 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 0.0000 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -1.5000 0.0000 C 0 0 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 -2.5981 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -0.0000 0.0000 C 0 0 1 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 0.8660 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -1.0000 0.0000 C 0 0 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 -0.0000 -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 -5.1962 -1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 15 1 0 0 0 0 2 15 1 0 0 0 0 3 16 1 0 0 0 0 4 28 1 0 0 0 0 5 28 1 0 0 0 0 6 7 1 0 0 0 0 6 8 1 0 0 0 0 7 15 2 0 0 0 0 8 16 1 0 0 0 0 9 11 1 0 0 0 0 9 16 2 0 0 0 0 10 12 2 0 0 0 0 10 17 1 0 0 0 0 11 18 1 0 0 0 0 12 21 1 0 0 0 0 13 17 2 0 0 0 0 13 19 1 0 0 0 0 14 20 1 0 0 0 0 14 22 1 0 0 0 0 17 29 1 0 0 0 0 18 24 2 0 0 0 0 18 26 1 0 0 0 0 19 21 2 0 0 0 0 19 25 1 0 0 0 0 20 24 1 0 0 0 0 20 27 2 0 0 0 0 21 33 1 0 0 0 0 22 28 1 0 0 0 0 22 30 1 1 0 0 0 23 25 1 0 0 0 0 23 26 2 0 0 0 0 23 27 1 0 0 0 0 24 31 1 0 0 0 0 25 32 2 0 0 0 0 26 33 1 0 0 0 0 27 34 1 0 0 0 0 28 34 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	464.22
Volume:	487.631
LogP:	6.623
LogD:	3.821
LogS:	-2.106
# Rotatable Bonds:	5
TPSA:	100.13
# H-Bond Aceptor:	6
# H-Bond Donor:	3
# Rings:	4
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.332
Synthetic Accessibility Score:	3.83
Fsp3:	0.393
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.831
MDCK Permeability:	1.4945566363167018e-05
Pgp-inhibitor:	0.824
Pgp-substrate:	0.987
Human Intestinal Absorption (HIA):	0.056
20% Bioavailability (F20%):	0.62
30% Bioavailability (F30%):	0.009

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.012
Plasma Protein Binding (PPB):	94.7146987915039%
Volume Distribution (VD):	0.367
Pgp-substrate:	3.8510055541992188%

ADMET: Metabolism

CYP1A2-inhibitor:	0.362
CYP1A2-substrate:	0.321
CYP2C19-inhibitor:	0.684
CYP2C19-substrate:	0.077
CYP2C9-inhibitor:	0.837
CYP2C9-substrate:	0.947
CYP2D6-inhibitor:	0.47
CYP2D6-substrate:	0.228
CYP3A4-inhibitor:	0.222
CYP3A4-substrate:	0.114

ADMET: Excretion

Clearance (CL):	4.621
Half-life (T1/2):	0.187

ADMET: Toxicity

hERG Blockers:	0.037
Human Hepatotoxicity (H-HT):	0.973
Drug-inuced Liver Injury (DILI):	0.562
AMES Toxicity:	0.02
Rat Oral Acute Toxicity:	0.94
Maximum Recommended Daily Dose:	0.962
Skin Sensitization:	0.764
Carcinogencity:	0.15
Eye Corrosion:	0.003
Eye Irritation:	0.051
Respiratory Toxicity:	0.728

Download Data

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

Natural Product: NPC3629

Natural Product ID:	NPC3629
*Common Name:**	Cochinensoxanthone
IUPAC Name:	(3S)-6-[(2E)-3,7-dimethylocta-2,6-dienyl]-3,5,10-trihydroxy-2,2-dimethyl-3,4-dihydropyrano[2,3-a]xanthen-12-one
Synonyms:	Cochinensoxanthone
Standard InCHIKey:	GZOFBXLMLDTZJM-NAVGAYGYSA-N
Standard InCHI:	InChI=1S/C28H32O6/c1-15(2)7-6-8-16(3)9-11-18-24(31)20-14-22(30)28(4,5)34-27(20)23-25(32)19-13-17(29)10-12-21(19)33-26(18)23/h7,9-10,12-13,22,29-31H,6,8,11,14H2,1-5H3/b16-9+/t22-/m0/s1
SMILES:	C/C(=CCc1c(O)c2C[C@H](O)C(Oc2c2c1oc1ccc(cc1c2=O)O)(C)C)/CCC=C(C)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL1782239
PubChem CID:	53355018
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0000123] Benzopyrans [CHEMONTID:0003410] 1-benzopyrans [CHEMONTID:0002817] Dibenzopyrans [CHEMONTID:0000200] Xanthenes [CHEMONTID:0000204] Xanthones [CHEMONTID:0003518] 4-prenylated xanthones

*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
NPO24928	Cratoxylum cochinchinense	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15182859]
NPO24928	Cratoxylum cochinchinense	Species	Hypericaceae	Eukaryota	n.a.	root	n.a.	PMID[16310231]
NPO24928	Cratoxylum cochinchinense	Species	Hypericaceae	Eukaryota	n.a.	root	n.a.	PMID[16651783]
NPO24928	Cratoxylum cochinchinense	Species	Hypericaceae	Eukaryota	n.a.	stem	n.a.	PMID[21428375]
NPO24928	Cratoxylum cochinchinense	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO24928	Cratoxylum cochinchinense	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO24928	Cratoxylum cochinchinense	Species	Hypericaceae	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
ED50	1

Activity Type	# Activity
Cell Line	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT139	Cell Line	HT-29	Homo sapiens	ED50	>	10.0	uM	PMID[451940]

☑ 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 NPC3629 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	415
0.1-0.2	1583
0.2-0.3	3729
0.3-0.4	9106
0.4-0.5	9320
0.5-0.6	3749
0.6-0.7	5262
0.7-0.8	4559
0.8-0.85	2330
0.85-0.9	2188
0.9-0.95	451
0.95-1	5

Similarity Score	Similarity Level	Natural Product ID
0.9934	High Similarity	NPC471976
0.9671	High Similarity	NPC477958
0.9539	High Similarity	NPC475790
0.9481	High Similarity	NPC78492
0.9481	High Similarity	NPC208152
0.9477	High Similarity	NPC7989
0.9477	High Similarity	NPC223701
0.9477	High Similarity	NPC472583
0.9477	High Similarity	NPC469405
0.9474	High Similarity	NPC471676
0.9474	High Similarity	NPC472422
0.9474	High Similarity	NPC244577
0.9474	High Similarity	NPC471677
0.9474	High Similarity	NPC474021
0.9474	High Similarity	NPC472420
0.9474	High Similarity	NPC474023
0.9474	High Similarity	NPC263384
0.9427	High Similarity	NPC220912
0.9427	High Similarity	NPC474034
0.9427	High Similarity	NPC474033
0.9363	High Similarity	NPC134783
0.9363	High Similarity	NPC228383
0.9363	High Similarity	NPC472632
0.9363	High Similarity	NPC471210
0.9359	High Similarity	NPC473990
0.9351	High Similarity	NPC293286
0.9342	High Similarity	NPC266499
0.9342	High Similarity	NPC223988
0.9342	High Similarity	NPC472628
0.9317	High Similarity	NPC103307
0.9313	High Similarity	NPC225419
0.9313	High Similarity	NPC6588
0.9313	High Similarity	NPC477154
0.9313	High Similarity	NPC117854
0.9308	High Similarity	NPC234052
0.9304	High Similarity	NPC472402
0.9304	High Similarity	NPC473961
0.9304	High Similarity	NPC472448
0.9304	High Similarity	NPC83922
0.9299	High Similarity	NPC174953
0.9299	High Similarity	NPC475784
0.9295	High Similarity	NPC471209
0.929	High Similarity	NPC304207
0.929	High Similarity	NPC259710
0.929	High Similarity	NPC477530
0.929	High Similarity	NPC48579
0.929	High Similarity	NPC217706
0.929	High Similarity	NPC470681
0.929	High Similarity	NPC207809
0.9286	High Similarity	NPC161881
0.9286	High Similarity	NPC171651
0.9286	High Similarity	NPC35567
0.9286	High Similarity	NPC477957
0.9286	High Similarity	NPC56232
0.9286	High Similarity	NPC243171
0.9286	High Similarity	NPC473996
0.9286	High Similarity	NPC150123
0.9286	High Similarity	NPC244583
0.9286	High Similarity	NPC138288
0.9286	High Similarity	NPC10807
0.9281	High Similarity	NPC37348
0.9281	High Similarity	NPC472633
0.9281	High Similarity	NPC101957
0.9281	High Similarity	NPC120105
0.9276	High Similarity	NPC186397
0.9276	High Similarity	NPC37135
0.9259	High Similarity	NPC121333
0.9255	High Similarity	NPC152477
0.925	High Similarity	NPC128293
0.925	High Similarity	NPC471213
0.925	High Similarity	NPC120593
0.925	High Similarity	NPC173292
0.9245	High Similarity	NPC124038
0.9241	High Similarity	NPC471211
0.9241	High Similarity	NPC74854
0.9241	High Similarity	NPC474038
0.9241	High Similarity	NPC472634
0.9241	High Similarity	NPC30655
0.9241	High Similarity	NPC167678
0.9241	High Similarity	NPC29876
0.9241	High Similarity	NPC471212
0.9241	High Similarity	NPC45124
0.9236	High Similarity	NPC250214
0.9236	High Similarity	NPC95936
0.9231	High Similarity	NPC215917
0.9231	High Similarity	NPC10754
0.9231	High Similarity	NPC20530
0.9226	High Similarity	NPC326592
0.9226	High Similarity	NPC248793
0.9226	High Similarity	NPC180301
0.9226	High Similarity	NPC209760
0.9226	High Similarity	NPC203080
0.9226	High Similarity	NPC112701
0.9226	High Similarity	NPC109594
0.9226	High Similarity	NPC100134
0.9221	High Similarity	NPC262039
0.9221	High Similarity	NPC262038
0.9221	High Similarity	NPC477897
0.9221	High Similarity	NPC472580
0.9221	High Similarity	NPC474772
0.9221	High Similarity	NPC254412
0.9221	High Similarity	NPC474744
0.9221	High Similarity	NPC472636
0.9221	High Similarity	NPC289774
0.9221	High Similarity	NPC328740
0.9221	High Similarity	NPC472423
0.9221	High Similarity	NPC278476
0.9221	High Similarity	NPC319910
0.9221	High Similarity	NPC209846
0.9216	High Similarity	NPC89442
0.9211	High Similarity	NPC472627
0.9211	High Similarity	NPC91902
0.9198	High Similarity	NPC74559
0.9193	High Similarity	NPC8965
0.9193	High Similarity	NPC14662
0.9187	High Similarity	NPC50960
0.9187	High Similarity	NPC293319
0.9187	High Similarity	NPC224280
0.9187	High Similarity	NPC62261
0.9182	High Similarity	NPC476247
0.9182	High Similarity	NPC261470
0.9177	High Similarity	NPC118256
0.9177	High Similarity	NPC204290
0.9177	High Similarity	NPC472631
0.9177	High Similarity	NPC472630
0.9177	High Similarity	NPC476980
0.9177	High Similarity	NPC192686
0.9177	High Similarity	NPC119209
0.9172	High Similarity	NPC474055
0.9172	High Similarity	NPC196448
0.9172	High Similarity	NPC476981
0.9172	High Similarity	NPC223787
0.9172	High Similarity	NPC99597
0.9172	High Similarity	NPC282390
0.9172	High Similarity	NPC162869
0.9172	High Similarity	NPC27337
0.9172	High Similarity	NPC48208
0.9172	High Similarity	NPC281137
0.9172	High Similarity	NPC475267
0.9172	High Similarity	NPC262286
0.9172	High Similarity	NPC36852
0.9172	High Similarity	NPC78225
0.9172	High Similarity	NPC474208
0.9172	High Similarity	NPC156057
0.9172	High Similarity	NPC284820
0.9172	High Similarity	NPC473272
0.9172	High Similarity	NPC291508
0.9172	High Similarity	NPC210084
0.9172	High Similarity	NPC472598
0.9172	High Similarity	NPC474836
0.9167	High Similarity	NPC111341
0.9167	High Similarity	NPC476169
0.9167	High Similarity	NPC37392
0.9167	High Similarity	NPC304745
0.9167	High Similarity	NPC113906
0.9167	High Similarity	NPC226025
0.9167	High Similarity	NPC321779
0.9161	High Similarity	NPC474843
0.9161	High Similarity	NPC216035
0.9161	High Similarity	NPC327269
0.9161	High Similarity	NPC285623
0.9161	High Similarity	NPC210597
0.9161	High Similarity	NPC31627
0.9161	High Similarity	NPC476238
0.9161	High Similarity	NPC217149
0.9156	High Similarity	NPC472421
0.9156	High Similarity	NPC177308
0.9156	High Similarity	NPC124478
0.9156	High Similarity	NPC105136
0.915	High Similarity	NPC160821
0.915	High Similarity	NPC132592
0.9145	High Similarity	NPC290133
0.9145	High Similarity	NPC187282
0.9145	High Similarity	NPC24136
0.9145	High Similarity	NPC472629
0.9145	High Similarity	NPC316769
0.9141	High Similarity	NPC212038
0.9141	High Similarity	NPC271848
0.9141	High Similarity	NPC81332
0.9141	High Similarity	NPC262580
0.9141	High Similarity	NPC289396
0.9136	High Similarity	NPC177480
0.9136	High Similarity	NPC242395
0.9136	High Similarity	NPC326877
0.913	High Similarity	NPC39091
0.913	High Similarity	NPC119589
0.913	High Similarity	NPC70441
0.9125	High Similarity	NPC152659
0.9125	High Similarity	NPC472625
0.9125	High Similarity	NPC236521
0.9125	High Similarity	NPC248638
0.9125	High Similarity	NPC7483
0.9125	High Similarity	NPC273959
0.9119	High Similarity	NPC474186
0.9119	High Similarity	NPC142252
0.9119	High Similarity	NPC26326
0.9119	High Similarity	NPC308992
0.9119	High Similarity	NPC198829
0.9119	High Similarity	NPC266314
0.9119	High Similarity	NPC474187

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 NPC3629 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	371
0.1-0.2	898
0.2-0.3	1727
0.3-0.4	2614
0.4-0.5	1877
0.5-0.6	1057
0.6-0.7	403
0.7-0.8	143
0.8-0.85	30
0.85-0.9	27
0.9-0.95	3
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.9156	High Similarity	NPD4380	Phase 2
0.9103	High Similarity	NPD2393	Clinical (unspecified phase)
0.8938	High Similarity	NPD5494	Approved
0.8931	High Similarity	NPD7075	Discontinued
0.8917	High Similarity	NPD1934	Approved
0.8861	High Similarity	NPD2801	Approved
0.8861	High Similarity	NPD7096	Clinical (unspecified phase)
0.8834	High Similarity	NPD6166	Phase 2
0.8834	High Similarity	NPD6168	Clinical (unspecified phase)
0.8834	High Similarity	NPD6167	Clinical (unspecified phase)
0.8812	High Similarity	NPD4381	Clinical (unspecified phase)
0.8788	High Similarity	NPD7804	Clinical (unspecified phase)
0.8735	High Similarity	NPD7074	Phase 3
0.871	High Similarity	NPD4378	Clinical (unspecified phase)
0.8688	High Similarity	NPD8443	Clinical (unspecified phase)
0.8684	High Similarity	NPD1549	Phase 2
0.8675	High Similarity	NPD7054	Approved
0.8625	High Similarity	NPD7819	Suspended
0.8623	High Similarity	NPD7472	Approved
0.8618	High Similarity	NPD1552	Clinical (unspecified phase)
0.8618	High Similarity	NPD1550	Clinical (unspecified phase)
0.859	High Similarity	NPD7410	Clinical (unspecified phase)
0.8571	High Similarity	NPD5402	Approved
0.8562	High Similarity	NPD6801	Discontinued
0.8537	High Similarity	NPD6959	Discontinued
0.8521	High Similarity	NPD7251	Discontinued
0.8519	High Similarity	NPD3882	Suspended
0.8519	High Similarity	NPD4868	Clinical (unspecified phase)
0.8503	High Similarity	NPD3818	Discontinued
0.85	High Similarity	NPD7411	Suspended
0.8471	Intermediate Similarity	NPD4338	Clinical (unspecified phase)
0.8471	Intermediate Similarity	NPD7808	Phase 3
0.8462	Intermediate Similarity	NPD6797	Phase 2
0.8452	Intermediate Similarity	NPD5844	Phase 1
0.8431	Intermediate Similarity	NPD2796	Approved
0.8412	Intermediate Similarity	NPD6559	Discontinued
0.8408	Intermediate Similarity	NPD1511	Approved
0.8366	Intermediate Similarity	NPD1510	Phase 2
0.8302	Intermediate Similarity	NPD1512	Approved
0.8295	Intermediate Similarity	NPD7879	Clinical (unspecified phase)
0.8291	Intermediate Similarity	NPD6799	Approved
0.8246	Intermediate Similarity	NPD7993	Clinical (unspecified phase)
0.8232	Intermediate Similarity	NPD3817	Phase 2
0.8224	Intermediate Similarity	NPD1240	Approved
0.8194	Intermediate Similarity	NPD2935	Discontinued
0.8182	Intermediate Similarity	NPD7768	Phase 2
0.8166	Intermediate Similarity	NPD7852	Clinical (unspecified phase)
0.8137	Intermediate Similarity	NPD5403	Approved
0.8118	Intermediate Similarity	NPD7473	Discontinued
0.8117	Intermediate Similarity	NPD1607	Approved
0.8098	Intermediate Similarity	NPD6599	Discontinued
0.8047	Intermediate Similarity	NPD6232	Discontinued
0.8024	Intermediate Similarity	NPD3749	Approved
0.8012	Intermediate Similarity	NPD5401	Approved
0.8	Intermediate Similarity	NPD8312	Approved
0.8	Intermediate Similarity	NPD8313	Approved
0.7988	Intermediate Similarity	NPD1247	Approved
0.7965	Intermediate Similarity	NPD3751	Discontinued
0.7952	Intermediate Similarity	NPD1465	Phase 2
0.7925	Intermediate Similarity	NPD7421	Clinical (unspecified phase)
0.7925	Intermediate Similarity	NPD2800	Approved
0.7901	Intermediate Similarity	NPD2532	Approved
0.7901	Intermediate Similarity	NPD2534	Approved
0.7901	Intermediate Similarity	NPD2533	Approved
0.788	Intermediate Similarity	NPD6778	Approved
0.788	Intermediate Similarity	NPD6781	Approved
0.788	Intermediate Similarity	NPD6779	Approved
0.788	Intermediate Similarity	NPD6780	Approved
0.788	Intermediate Similarity	NPD6777	Approved
0.788	Intermediate Similarity	NPD6782	Approved
0.788	Intermediate Similarity	NPD6776	Approved
0.7875	Intermediate Similarity	NPD4628	Phase 3
0.7875	Intermediate Similarity	NPD3750	Approved
0.7849	Intermediate Similarity	NPD7697	Approved
0.7849	Intermediate Similarity	NPD7696	Phase 3
0.7849	Intermediate Similarity	NPD7435	Discontinued
0.7849	Intermediate Similarity	NPD7698	Approved
0.7836	Intermediate Similarity	NPD3787	Discontinued
0.7816	Intermediate Similarity	NPD7286	Phase 2
0.7805	Intermediate Similarity	NPD920	Approved
0.7784	Intermediate Similarity	NPD6844	Discontinued
0.7778	Intermediate Similarity	NPD7701	Phase 2
0.7778	Intermediate Similarity	NPD8397	Clinical (unspecified phase)
0.7765	Intermediate Similarity	NPD8150	Discontinued
0.7756	Intermediate Similarity	NPD1613	Approved
0.7756	Intermediate Similarity	NPD943	Approved
0.7756	Intermediate Similarity	NPD1612	Clinical (unspecified phase)
0.775	Intermediate Similarity	NPD970	Clinical (unspecified phase)
0.7749	Intermediate Similarity	NPD7783	Phase 2
0.7749	Intermediate Similarity	NPD7782	Clinical (unspecified phase)
0.7742	Intermediate Similarity	NPD6859	Clinical (unspecified phase)
0.7736	Intermediate Similarity	NPD6099	Approved
0.7736	Intermediate Similarity	NPD6100	Approved
0.7736	Intermediate Similarity	NPD1551	Phase 2
0.7727	Intermediate Similarity	NPD5953	Discontinued
0.7725	Intermediate Similarity	NPD7584	Approved
0.7717	Intermediate Similarity	NPD8090	Clinical (unspecified phase)
0.7713	Intermediate Similarity	NPD7871	Phase 2
0.7713	Intermediate Similarity	NPD7870	Phase 2
0.7711	Intermediate Similarity	NPD3226	Approved
0.7701	Intermediate Similarity	NPD6823	Phase 2
0.7688	Intermediate Similarity	NPD2346	Discontinued
0.7683	Intermediate Similarity	NPD642	Clinical (unspecified phase)
0.7676	Intermediate Similarity	NPD7699	Phase 2
0.7676	Intermediate Similarity	NPD7700	Phase 2
0.7673	Intermediate Similarity	NPD1509	Clinical (unspecified phase)
0.7673	Intermediate Similarity	NPD2799	Discontinued
0.7667	Intermediate Similarity	NPD8434	Phase 2
0.7661	Intermediate Similarity	NPD919	Approved
0.7658	Intermediate Similarity	NPD6651	Approved
0.7654	Intermediate Similarity	NPD1878	Clinical (unspecified phase)
0.7654	Intermediate Similarity	NPD6398	Clinical (unspecified phase)
0.7644	Intermediate Similarity	NPD8151	Discontinued
0.764	Intermediate Similarity	NPD4419	Clinical (unspecified phase)
0.7628	Intermediate Similarity	NPD4907	Clinical (unspecified phase)
0.7628	Intermediate Similarity	NPD2313	Discontinued
0.7611	Intermediate Similarity	NPD8055	Clinical (unspecified phase)
0.7609	Intermediate Similarity	NPD6534	Approved
0.7609	Intermediate Similarity	NPD4363	Phase 3
0.7609	Intermediate Similarity	NPD4360	Phase 2
0.7609	Intermediate Similarity	NPD6535	Approved
0.7604	Intermediate Similarity	NPD7874	Approved
0.7604	Intermediate Similarity	NPD7875	Clinical (unspecified phase)
0.7594	Intermediate Similarity	NPD7501	Clinical (unspecified phase)
0.7593	Intermediate Similarity	NPD1243	Approved
0.7586	Intermediate Similarity	NPD3926	Phase 2
0.7578	Intermediate Similarity	NPD2344	Approved
0.7565	Intermediate Similarity	NPD7801	Approved
0.7562	Intermediate Similarity	NPD3748	Approved
0.7561	Intermediate Similarity	NPD643	Clinical (unspecified phase)
0.7531	Intermediate Similarity	NPD2424	Discontinued
0.7529	Intermediate Similarity	NPD8455	Phase 2
0.7515	Intermediate Similarity	NPD7390	Discontinued
0.7515	Intermediate Similarity	NPD7615	Clinical (unspecified phase)
0.75	Intermediate Similarity	NPD1529	Clinical (unspecified phase)
0.75	Intermediate Similarity	NPD6190	Approved
0.75	Intermediate Similarity	NPD5808	Clinical (unspecified phase)
0.75	Intermediate Similarity	NPD1547	Clinical (unspecified phase)
0.75	Intermediate Similarity	NPD4908	Phase 1
0.7484	Intermediate Similarity	NPD5123	Clinical (unspecified phase)
0.7484	Intermediate Similarity	NPD5124	Phase 1
0.7484	Intermediate Similarity	NPD230	Phase 1
0.747	Intermediate Similarity	NPD7004	Clinical (unspecified phase)
0.7458	Intermediate Similarity	NPD7228	Approved
0.7453	Intermediate Similarity	NPD7033	Discontinued
0.7452	Intermediate Similarity	NPD3027	Phase 3
0.744	Intermediate Similarity	NPD1653	Approved
0.7436	Intermediate Similarity	NPD1530	Clinical (unspecified phase)
0.7429	Intermediate Similarity	NPD5711	Approved
0.7429	Intermediate Similarity	NPD5710	Approved
0.7396	Intermediate Similarity	NPD7458	Discontinued
0.7394	Intermediate Similarity	NPD2309	Approved
0.7389	Intermediate Similarity	NPD7685	Pre-registration
0.7389	Intermediate Similarity	NPD6832	Phase 2
0.7381	Intermediate Similarity	NPD6980	Clinical (unspecified phase)
0.7375	Intermediate Similarity	NPD447	Suspended
0.7344	Intermediate Similarity	NPD8319	Approved
0.7344	Intermediate Similarity	NPD8320	Phase 1
0.7342	Intermediate Similarity	NPD4625	Phase 3
0.7333	Intermediate Similarity	NPD3823	Discontinued
0.733	Intermediate Similarity	NPD7229	Phase 3
0.7326	Intermediate Similarity	NPD5761	Phase 2
0.7326	Intermediate Similarity	NPD5760	Phase 2
0.7325	Intermediate Similarity	NPD2861	Phase 2
0.732	Intermediate Similarity	NPD7585	Approved
0.7308	Intermediate Similarity	NPD1203	Approved
0.7296	Intermediate Similarity	NPD6410	Clinical (unspecified phase)
0.7273	Intermediate Similarity	NPD6212	Phase 3
0.7273	Intermediate Similarity	NPD6213	Phase 3
0.7273	Intermediate Similarity	NPD1610	Phase 2
0.7273	Intermediate Similarity	NPD7199	Phase 2
0.7273	Intermediate Similarity	NPD6214	Clinical (unspecified phase)
0.7268	Intermediate Similarity	NPD7583	Approved
0.7267	Intermediate Similarity	NPD37	Approved
0.7267	Intermediate Similarity	NPD1899	Clinical (unspecified phase)
0.7257	Intermediate Similarity	NPD6234	Discontinued
0.725	Intermediate Similarity	NPD6233	Phase 2
0.7241	Intermediate Similarity	NPD4967	Phase 2
0.7241	Intermediate Similarity	NPD4965	Approved
0.7241	Intermediate Similarity	NPD4966	Approved
0.7239	Intermediate Similarity	NPD651	Clinical (unspecified phase)
0.7228	Intermediate Similarity	NPD8155	Clinical (unspecified phase)
0.7196	Intermediate Similarity	NPD4362	Clinical (unspecified phase)
0.7196	Intermediate Similarity	NPD4361	Phase 2
0.7188	Intermediate Similarity	NPD6798	Discontinued
0.7169	Intermediate Similarity	NPD5698	Clinical (unspecified phase)
0.7169	Intermediate Similarity	NPD1652	Phase 2
0.716	Intermediate Similarity	NPD4662	Approved
0.716	Intermediate Similarity	NPD4661	Approved
0.716	Intermediate Similarity	NPD6355	Discontinued
0.716	Intermediate Similarity	NPD1933	Approved
0.7152	Intermediate Similarity	NPD7266	Discontinued
0.7152	Intermediate Similarity	NPD2798	Approved
0.7151	Intermediate Similarity	NPD7784	Clinical (unspecified phase)
0.7134	Intermediate Similarity	NPD4308	Phase 3
0.7124	Intermediate Similarity	NPD1548	Phase 1
0.7118	Intermediate Similarity	NPD6273	Approved
0.7115	Intermediate Similarity	NPD9717	Approved
0.7112	Intermediate Similarity	NPD4287	Approved
0.7107	Intermediate Similarity	NPD9494	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