NPASS Compound

Structure

NPC473962 OpenBabel07101719252D 34 39 0 0 1 0 0 0 0 0999 V2000 -6.6729 -4.9625 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8366 -2.9945 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0279 -4.4081 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.3346 -6.4488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0475 -5.2898 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7431 0.6691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7653 -1.8171 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0962 -2.5602 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4563 -0.8660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1180 -2.3523 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7026 -0.4945 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5686 -0.9945 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9735 -2.9945 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.3857 -2.1855 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7026 -3.4945 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5686 -3.9945 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9706 -2.4945 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1045 -1.9945 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9706 -0.4945 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.6947 -4.7546 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.8366 -0.9945 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.5686 -1.9945 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.4781 -0.6581 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.3857 -3.8035 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.4347 -2.4945 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.7026 -2.4945 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8090 -1.4013 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9781 0.2079 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8366 -1.9945 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.4347 -3.4945 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.1045 -0.9945 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.0256 -5.4977 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1.3849 1.1215 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4 32 1 0 0 0 0 5 32 1 0 0 0 0 6 33 1 0 0 0 0 7 8 2 0 0 0 0 7 9 1 0 0 0 0 8 10 1 0 0 0 0 9 23 2 0 0 0 0 10 27 2 0 0 0 0 11 12 1 0 0 0 0 11 21 1 0 0 0 0 13 14 1 0 0 0 0 13 24 1 0 0 0 0 14 25 1 0 0 0 0 15 16 1 0 0 0 0 15 26 1 0 0 0 0 16 30 1 0 0 0 0 17 18 1 0 0 0 0 17 29 1 0 0 0 0 19 21 1 0 0 0 0 19 31 1 0 0 0 0 20 1 1 1 0 0 0 20 24 1 0 0 0 0 20 32 1 0 0 0 0 21 29 1 1 0 0 0 22 12 1 6 0 0 0 22 25 1 0 0 0 0 22 26 1 0 0 0 0 23 27 1 0 0 0 0 23 28 1 0 0 0 0 24 30 1 1 0 0 0 25 30 1 1 0 0 0 26 29 1 1 0 0 0 27 31 1 0 0 0 0 28 33 1 0 0 0 0 28 34 2 0 0 0 0 29 2 1 1 0 0 0 30 3 1 1 0 0 0 31 18 1 6 0 0 0 31 33 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	462.36
Volume:	513.631
LogP:	6.688
LogD:	4.81
LogS:	-5.991
# Rotatable Bonds:	2
TPSA:	23.55
# H-Bond Aceptor:	3
# H-Bond Donor:	0
# Rings:	6
# Heavy Atoms:	3

MedChem Properties

QED Drug-Likeness Score:	0.496
Synthetic Accessibility Score:	5.052
Fsp3:	0.774
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:	-4.749
MDCK Permeability:	1.1348645784892142e-05
Pgp-inhibitor:	0.999
Pgp-substrate:	0.236
Human Intestinal Absorption (HIA):	0.024
20% Bioavailability (F20%):	0.068
30% Bioavailability (F30%):	0.847

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.249
Plasma Protein Binding (PPB):	85.14474487304688%
Volume Distribution (VD):	2.521
Pgp-substrate:	6.243382453918457%

ADMET: Metabolism

CYP1A2-inhibitor:	0.161
CYP1A2-substrate:	0.524
CYP2C19-inhibitor:	0.142
CYP2C19-substrate:	0.983
CYP2C9-inhibitor:	0.326
CYP2C9-substrate:	0.218
CYP2D6-inhibitor:	0.945
CYP2D6-substrate:	0.909
CYP3A4-inhibitor:	0.94
CYP3A4-substrate:	0.92

ADMET: Excretion

Clearance (CL):	10.027
Half-life (T1/2):	0.147

ADMET: Toxicity

hERG Blockers:	0.958
Human Hepatotoxicity (H-HT):	0.292
Drug-inuced Liver Injury (DILI):	0.708
AMES Toxicity:	0.119
Rat Oral Acute Toxicity:	0.941
Maximum Recommended Daily Dose:	0.871
Skin Sensitization:	0.941
Carcinogencity:	0.75
Eye Corrosion:	0.016
Eye Irritation:	0.019
Respiratory Toxicity:	0.974

Download Data

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

Natural Product: NPC473962

Natural Product ID:	NPC473962
*Common Name:**	(+)-Spiropachysine
IUPAC Name:	(3R,5S,8R,9S,10S,13S,14S,17S)-17-[(1S)-1-(dimethylamino)ethyl]-2',10,13-trimethylspiro[1,2,4,5,6,7,8,9,11,12,14,15,16,17-tetradecahydrocyclopenta[a]phenanthrene-3,3'-isoindole]-1'-one
Synonyms:	(+)-Spiropachysine
Standard InCHIKey:	SLGWGPQWJRVPAD-PZOAWPBASA-N
Standard InCHI:	InChI=1S/C31H46N2O/c1-20(32(4)5)24-13-14-25-22-12-11-21-19-31(27-10-8-7-9-23(27)28(34)33(31)6)18-17-29(21,2)26(22)15-16-30(24,25)3/h7-10,20-22,24-26H,11-19H2,1-6H3/t20-,21-,22-,24+,25-,26-,29-,30+,31+/m0/s1
SMILES:	CN([C@H]([C@H]1CC[C@@H]2[C@]1(C)CC[C@H]1[C@H]2CC[C@@H]2[C@]1(C)CC[C@]1(C2)N(C)C(=O)c2c1cccc2)C)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL456512
PubChem CID:	209254
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0002340] Azasteroids 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
NPO4994	Pachysandra procumbens	Species	Buxaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[9784163]
NPO4994	Pachysandra procumbens	Species	Buxaceae	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	1

Activity Type	# Activity
Protein Complex	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT3844	Protein Complex	Anti-estrogen binding site (AEBS)	Homo sapiens	IC50	=	7400.0	nM	PMID[479627]

☑ 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 NPC473962 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	367
0.1-0.2	1659
0.2-0.3	5719
0.3-0.4	21525
0.4-0.5	11158
0.5-0.6	2077
0.6-0.7	164
0.7-0.8	22
0.8-0.85	1
0.85-0.9	2
0.9-0.95	1
0.95-1	2

Similarity Score	Similarity Level	Natural Product ID
0.9512	High Similarity	NPC79698
0.9141	High Similarity	NPC126458
0.8548	High Similarity	NPC473573
0.8468	Intermediate Similarity	NPC246904
0.7886	Intermediate Similarity	NPC474695
0.7722	Intermediate Similarity	NPC475427
0.7647	Intermediate Similarity	NPC73644
0.7619	Intermediate Similarity	NPC55529
0.7419	Intermediate Similarity	NPC474582
0.7081	Intermediate Similarity	NPC63047
0.7081	Intermediate Similarity	NPC475248
0.6923	Remote Similarity	NPC167336
0.6859	Remote Similarity	NPC66936
0.6822	Remote Similarity	NPC239854
0.6794	Remote Similarity	NPC473418
0.6776	Remote Similarity	NPC471516
0.6755	Remote Similarity	NPC130251
0.6746	Remote Similarity	NPC286994
0.6742	Remote Similarity	NPC472699
0.6742	Remote Similarity	NPC472700
0.6711	Remote Similarity	NPC301760
0.6693	Remote Similarity	NPC219573
0.6693	Remote Similarity	NPC185208
0.6692	Remote Similarity	NPC472683
0.6692	Remote Similarity	NPC472696
0.6692	Remote Similarity	NPC472701
0.6692	Remote Similarity	NPC472695
0.6689	Remote Similarity	NPC153007
0.6667	Remote Similarity	NPC212799
0.6667	Remote Similarity	NPC225319
0.6646	Remote Similarity	NPC222029
0.6646	Remote Similarity	NPC104345
0.6641	Remote Similarity	NPC471829
0.6641	Remote Similarity	NPC475939
0.6641	Remote Similarity	NPC472691
0.6641	Remote Similarity	NPC474866
0.6626	Remote Similarity	NPC469741
0.6615	Remote Similarity	NPC476993
0.6614	Remote Similarity	NPC256452
0.6599	Remote Similarity	NPC179224
0.6596	Remote Similarity	NPC226143
0.6579	Remote Similarity	NPC469560
0.6573	Remote Similarity	NPC109151
0.6556	Remote Similarity	NPC471123
0.6549	Remote Similarity	NPC27833
0.6536	Remote Similarity	NPC315051
0.6512	Remote Similarity	NPC239185
0.6508	Remote Similarity	NPC470926
0.6507	Remote Similarity	NPC119326
0.6494	Remote Similarity	NPC186284
0.6494	Remote Similarity	NPC22082
0.6463	Remote Similarity	NPC201424
0.6462	Remote Similarity	NPC134882
0.6457	Remote Similarity	NPC323420
0.6457	Remote Similarity	NPC59677
0.6433	Remote Similarity	NPC313850
0.6424	Remote Similarity	NPC162417
0.6424	Remote Similarity	NPC99632
0.6424	Remote Similarity	NPC282339
0.6424	Remote Similarity	NPC316104
0.6424	Remote Similarity	NPC476750
0.6423	Remote Similarity	NPC147513
0.6419	Remote Similarity	NPC473322
0.641	Remote Similarity	NPC469537
0.6385	Remote Similarity	NPC265220
0.6377	Remote Similarity	NPC181390
0.6371	Remote Similarity	NPC157479
0.6364	Remote Similarity	NPC472879
0.6364	Remote Similarity	NPC109514
0.6336	Remote Similarity	NPC75724
0.6335	Remote Similarity	NPC154602
0.6335	Remote Similarity	NPC243756
0.6333	Remote Similarity	NPC255447
0.6331	Remote Similarity	NPC476749
0.6328	Remote Similarity	NPC1682
0.6328	Remote Similarity	NPC188844
0.632	Remote Similarity	NPC305602
0.632	Remote Similarity	NPC17497
0.6319	Remote Similarity	NPC200964
0.6319	Remote Similarity	NPC161956
0.6319	Remote Similarity	NPC112373
0.6319	Remote Similarity	NPC258531
0.6312	Remote Similarity	NPC109787
0.6296	Remote Similarity	NPC122106
0.6296	Remote Similarity	NPC285381
0.6291	Remote Similarity	NPC207428
0.6282	Remote Similarity	NPC471164
0.6279	Remote Similarity	NPC474974
0.6277	Remote Similarity	NPC470252
0.6276	Remote Similarity	NPC257490
0.6276	Remote Similarity	NPC314192
0.627	Remote Similarity	NPC267262
0.6267	Remote Similarity	NPC200589
0.6265	Remote Similarity	NPC315368
0.6257	Remote Similarity	NPC214626
0.6257	Remote Similarity	NPC96901
0.6257	Remote Similarity	NPC251212
0.6257	Remote Similarity	NPC139085
0.625	Remote Similarity	NPC45033
0.625	Remote Similarity	NPC284475
0.625	Remote Similarity	NPC291962
0.625	Remote Similarity	NPC177684
0.6242	Remote Similarity	NPC113946
0.6242	Remote Similarity	NPC470648
0.6241	Remote Similarity	NPC33742
0.6231	Remote Similarity	NPC260233
0.6231	Remote Similarity	NPC472880
0.622	Remote Similarity	NPC113307
0.622	Remote Similarity	NPC298115
0.6213	Remote Similarity	NPC279527
0.6213	Remote Similarity	NPC214960
0.6212	Remote Similarity	NPC49994
0.6209	Remote Similarity	NPC266425
0.6202	Remote Similarity	NPC153885
0.6202	Remote Similarity	NPC473661
0.62	Remote Similarity	NPC472678
0.6199	Remote Similarity	NPC355
0.6184	Remote Similarity	NPC53044
0.6181	Remote Similarity	NPC472698
0.6181	Remote Similarity	NPC220698
0.6181	Remote Similarity	NPC264580
0.6181	Remote Similarity	NPC472697
0.6176	Remote Similarity	NPC143516
0.6172	Remote Similarity	NPC19256
0.617	Remote Similarity	NPC276949
0.617	Remote Similarity	NPC35850
0.6163	Remote Similarity	NPC473743
0.616	Remote Similarity	NPC182106
0.616	Remote Similarity	NPC311769
0.6154	Remote Similarity	NPC289883
0.6154	Remote Similarity	NPC238219
0.6154	Remote Similarity	NPC315276
0.6154	Remote Similarity	NPC71140
0.6154	Remote Similarity	NPC246757
0.6154	Remote Similarity	NPC239357
0.6154	Remote Similarity	NPC285926
0.6154	Remote Similarity	NPC83214
0.6154	Remote Similarity	NPC472106
0.6154	Remote Similarity	NPC14672
0.6154	Remote Similarity	NPC291070
0.6136	Remote Similarity	NPC472258
0.6133	Remote Similarity	NPC152850
0.6133	Remote Similarity	NPC89923
0.6133	Remote Similarity	NPC71933
0.6133	Remote Similarity	NPC239990
0.6133	Remote Similarity	NPC478079
0.6133	Remote Similarity	NPC105114
0.6131	Remote Similarity	NPC130898
0.6131	Remote Similarity	NPC472117
0.6131	Remote Similarity	NPC474973
0.6131	Remote Similarity	NPC474804
0.6131	Remote Similarity	NPC472120
0.6131	Remote Similarity	NPC472101
0.6124	Remote Similarity	NPC125226
0.6124	Remote Similarity	NPC133461
0.6115	Remote Similarity	NPC150712
0.6111	Remote Similarity	NPC470545
0.6108	Remote Similarity	NPC276085
0.6107	Remote Similarity	NPC329430
0.6107	Remote Similarity	NPC470343
0.6107	Remote Similarity	NPC472244
0.6104	Remote Similarity	NPC132847
0.6098	Remote Similarity	NPC231986
0.6098	Remote Similarity	NPC90150
0.6093	Remote Similarity	NPC116057
0.6093	Remote Similarity	NPC150863
0.609	Remote Similarity	NPC122553
0.609	Remote Similarity	NPC316906
0.6087	Remote Similarity	NPC473541
0.6084	Remote Similarity	NPC29285
0.6082	Remote Similarity	NPC473484
0.6077	Remote Similarity	NPC475057
0.6077	Remote Similarity	NPC155232
0.6076	Remote Similarity	NPC471574
0.6076	Remote Similarity	NPC161069
0.6074	Remote Similarity	NPC58200
0.6074	Remote Similarity	NPC470274
0.6071	Remote Similarity	NPC309531
0.6071	Remote Similarity	NPC265513
0.6071	Remote Similarity	NPC472102
0.6071	Remote Similarity	NPC248117
0.6069	Remote Similarity	NPC242269
0.6069	Remote Similarity	NPC470546
0.6067	Remote Similarity	NPC322433
0.6067	Remote Similarity	NPC136453
0.6065	Remote Similarity	NPC151706
0.6065	Remote Similarity	NPC475318
0.6065	Remote Similarity	NPC49577
0.6065	Remote Similarity	NPC474855
0.6065	Remote Similarity	NPC9687
0.6065	Remote Similarity	NPC293377
0.6065	Remote Similarity	NPC76785
0.6065	Remote Similarity	NPC476102
0.6065	Remote Similarity	NPC118099
0.6065	Remote Similarity	NPC300299
0.6065	Remote Similarity	NPC475598
0.6065	Remote Similarity	NPC273907
0.6065	Remote Similarity	NPC474811
0.6065	Remote Similarity	NPC79465
0.6065	Remote Similarity	NPC260045

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 NPC473962 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	219
0.1-0.2	687
0.2-0.3	794
0.3-0.4	2743
0.4-0.5	3343
0.5-0.6	1164
0.6-0.7	181
0.7-0.8	16
0.8-0.85	3
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.7836	Intermediate Similarity	NPD3549	Approved
0.7836	Intermediate Similarity	NPD3547	Approved
0.7836	Intermediate Similarity	NPD3550	Clinical (unspecified phase)
0.7721	Intermediate Similarity	NPD5653	Discontinued
0.75	Intermediate Similarity	NPD813	Approved
0.75	Intermediate Similarity	NPD7679	Phase 2
0.75	Intermediate Similarity	NPD2754	Discontinued
0.7432	Intermediate Similarity	NPD8239	Clinical (unspecified phase)
0.7388	Intermediate Similarity	NPD6345	Approved
0.7388	Intermediate Similarity	NPD6343	Approved
0.736	Intermediate Similarity	NPD4803	Discontinued
0.7348	Intermediate Similarity	NPD3551	Approved
0.7266	Intermediate Similarity	NPD6330	Clinical (unspecified phase)
0.7266	Intermediate Similarity	NPD6792	Phase 3
0.7219	Intermediate Similarity	NPD8165	Discontinued
0.7188	Intermediate Similarity	NPD2192	Approved
0.7188	Intermediate Similarity	NPD2197	Approved
0.7185	Intermediate Similarity	NPD5990	Approved
0.7185	Intermediate Similarity	NPD5991	Approved
0.7162	Intermediate Similarity	NPD2010	Phase 3
0.7143	Intermediate Similarity	NPD7254	Discontinued
0.7123	Intermediate Similarity	NPD7192	Discontinued
0.7087	Intermediate Similarity	NPD2196	Discontinued
0.7075	Intermediate Similarity	NPD7541	Clinical (unspecified phase)
0.7075	Intermediate Similarity	NPD4705	Clinical (unspecified phase)
0.7067	Intermediate Similarity	NPD2820	Phase 3
0.7063	Intermediate Similarity	NPD742	Approved
0.7037	Intermediate Similarity	NPD1323	Discontinued
0.7034	Intermediate Similarity	NPD7578	Phase 2
0.7034	Intermediate Similarity	NPD6740	Clinical (unspecified phase)
0.7029	Intermediate Similarity	NPD6806	Phase 1
0.7029	Intermediate Similarity	NPD5836	Discontinued
0.7023	Intermediate Similarity	NPD8009	Approved
0.7023	Intermediate Similarity	NPD8010	Approved
0.702	Intermediate Similarity	NPD7949	Clinical (unspecified phase)
0.7	Intermediate Similarity	NPD6566	Discontinued
0.7	Intermediate Similarity	NPD2365	Approved
0.6987	Remote Similarity	NPD2790	Discontinued
0.6984	Remote Similarity	NPD466	Approved
0.697	Remote Similarity	NPD3581	Discontinued
0.6966	Remote Similarity	NPD2846	Clinical (unspecified phase)
0.6963	Remote Similarity	NPD2508	Discontinued
0.6963	Remote Similarity	NPD853	Approved
0.6963	Remote Similarity	NPD851	Approved
0.6957	Remote Similarity	NPD1217	Clinical (unspecified phase)
0.6953	Remote Similarity	NPD6027	Approved
0.6953	Remote Similarity	NPD6024	Approved
0.6944	Remote Similarity	NPD3063	Discontinued
0.6929	Remote Similarity	NPD3624	Phase 2
0.6923	Remote Similarity	NPD1761	Approved
0.6923	Remote Similarity	NPD1766	Approved
0.6923	Remote Similarity	NPD1767	Approved
0.6923	Remote Similarity	NPD1765	Approved
0.6923	Remote Similarity	NPD1763	Approved
0.6918	Remote Similarity	NPD941	Approved
0.6913	Remote Similarity	NPD6655	Clinical (unspecified phase)
0.6905	Remote Similarity	NPD4655	Approved
0.6905	Remote Similarity	NPD4657	Approved
0.6901	Remote Similarity	NPD1482	Clinical (unspecified phase)
0.6901	Remote Similarity	NPD2634	Clinical (unspecified phase)
0.6892	Remote Similarity	NPD8125	Discontinued
0.6887	Remote Similarity	NPD6768	Approved
0.6875	Remote Similarity	NPD4549	Discontinued
0.6867	Remote Similarity	NPD5068	Clinical (unspecified phase)
0.6863	Remote Similarity	NPD7602	Clinical (unspecified phase)
0.6863	Remote Similarity	NPD7575	Phase 3
0.6853	Remote Similarity	NPD3245	Phase 3
0.6853	Remote Similarity	NPD3244	Pre-registration
0.6829	Remote Similarity	NPD7795	Phase 2
0.6822	Remote Similarity	NPD2193	Phase 2
0.6822	Remote Similarity	NPD2648	Phase 3
0.6818	Remote Similarity	NPD1956	Clinical (unspecified phase)
0.6797	Remote Similarity	NPD787	Suspended
0.6797	Remote Similarity	NPD7487	Discontinued
0.6794	Remote Similarity	NPD1677	Discontinued
0.6792	Remote Similarity	NPD6855	Clinical (unspecified phase)
0.6774	Remote Similarity	NPD7794	Clinical (unspecified phase)
0.6772	Remote Similarity	NPD1100	Approved
0.6772	Remote Similarity	NPD1099	Approved
0.6753	Remote Similarity	NPD5933	Phase 3
0.6753	Remote Similarity	NPD5932	Phase 3
0.6753	Remote Similarity	NPD5931	Phase 3
0.675	Remote Similarity	NPD7011	Discontinued
0.6746	Remote Similarity	NPD4094	Approved
0.6738	Remote Similarity	NPD1302	Clinical (unspecified phase)
0.6732	Remote Similarity	NPD5010	Approved
0.6732	Remote Similarity	NPD5009	Approved
0.6711	Remote Similarity	NPD7720	Phase 2
0.6692	Remote Similarity	NPD6588	Clinical (unspecified phase)
0.6692	Remote Similarity	NPD2171	Approved
0.6691	Remote Similarity	NPD3806	Clinical (unspecified phase)
0.6689	Remote Similarity	NPD7142	Discontinued
0.6667	Remote Similarity	NPD6817	Clinical (unspecified phase)
0.6667	Remote Similarity	NPD5227	Clinical (unspecified phase)
0.6645	Remote Similarity	NPD6485	Discontinued
0.6642	Remote Similarity	NPD3598	Phase 3
0.6641	Remote Similarity	NPD5597	Approved
0.6641	Remote Similarity	NPD5598	Approved
0.6625	Remote Similarity	NPD7072	Phase 2
0.6625	Remote Similarity	NPD7954	Clinical (unspecified phase)
0.6623	Remote Similarity	NPD7082	Approved
0.6621	Remote Similarity	NPD1321	Clinical (unspecified phase)
0.662	Remote Similarity	NPD1123	Approved
0.662	Remote Similarity	NPD1124	Approved
0.6615	Remote Similarity	NPD5630	Phase 1
0.6603	Remote Similarity	NPD1524	Phase 1
0.6597	Remote Similarity	NPD7464	Phase 3
0.6587	Remote Similarity	NPD7663	Clinical (unspecified phase)
0.6581	Remote Similarity	NPD5918	Discontinued
0.6581	Remote Similarity	NPD7259	Approved
0.6562	Remote Similarity	NPD7612	Clinical (unspecified phase)
0.6552	Remote Similarity	NPD5577	Clinical (unspecified phase)
0.6552	Remote Similarity	NPD5578	Approved
0.6547	Remote Similarity	NPD1025	Discontinued
0.6538	Remote Similarity	NPD7295	Approved
0.6522	Remote Similarity	NPD1175	Approved
0.6519	Remote Similarity	NPD4939	Clinical (unspecified phase)
0.6515	Remote Similarity	NPD3357	Discontinued
0.6513	Remote Similarity	NPD6342	Discontinued
0.6512	Remote Similarity	NPD3495	Discontinued
0.6503	Remote Similarity	NPD5187	Clinical (unspecified phase)
0.6497	Remote Similarity	NPD6884	Clinical (unspecified phase)
0.6486	Remote Similarity	NPD2919	Clinical (unspecified phase)
0.6486	Remote Similarity	NPD2918	Clinical (unspecified phase)
0.6478	Remote Similarity	NPD6144	Discontinued
0.6475	Remote Similarity	NPD3867	Phase 2
0.6467	Remote Similarity	NPD7086	Phase 2
0.6466	Remote Similarity	NPD2577	Clinical (unspecified phase)
0.6458	Remote Similarity	NPD4775	Clinical (unspecified phase)
0.6457	Remote Similarity	NPD4407	Approved
0.6457	Remote Similarity	NPD4405	Approved
0.6457	Remote Similarity	NPD4408	Approved
0.6456	Remote Similarity	NPD7478	Approved
0.6454	Remote Similarity	NPD7610	Discontinued
0.6449	Remote Similarity	NPD480	Approved
0.6442	Remote Similarity	NPD3589	Clinical (unspecified phase)
0.642	Remote Similarity	NPD7683	Discontinued
0.6415	Remote Similarity	NPD979	Approved
0.6414	Remote Similarity	NPD6408	Phase 1
0.6412	Remote Similarity	NPD1946	Clinical (unspecified phase)
0.641	Remote Similarity	NPD4464	Clinical (unspecified phase)
0.6406	Remote Similarity	NPD2878	Approved
0.6405	Remote Similarity	NPD6358	Phase 2
0.6403	Remote Similarity	NPD5181	Approved
0.6403	Remote Similarity	NPD5179	Approved
0.6403	Remote Similarity	NPD5180	Approved
0.64	Remote Similarity	NPD5581	Approved
0.6395	Remote Similarity	NPD6565	Approved
0.6395	Remote Similarity	NPD6563	Approved
0.6395	Remote Similarity	NPD6564	Approved
0.6389	Remote Similarity	NPD3836	Clinical (unspecified phase)
0.6382	Remote Similarity	NPD8643	Discontinued
0.6377	Remote Similarity	NPD753	Approved
0.6377	Remote Similarity	NPD2124	Approved
0.637	Remote Similarity	NPD1640	Clinical (unspecified phase)
0.6364	Remote Similarity	NPD3543	Discontinued
0.6358	Remote Similarity	NPD2950	Approved
0.6358	Remote Similarity	NPD2949	Approved
0.6358	Remote Similarity	NPD5086	Approved
0.6358	Remote Similarity	NPD7713	Phase 3
0.6358	Remote Similarity	NPD4680	Discontinued
0.6358	Remote Similarity	NPD7448	Suspended
0.6357	Remote Similarity	NPD4766	Approved
0.6353	Remote Similarity	NPD7854	Phase 2
0.6352	Remote Similarity	NPD6631	Clinical (unspecified phase)
0.6352	Remote Similarity	NPD7088	Discontinued
0.6351	Remote Similarity	NPD5339	Clinical (unspecified phase)
0.635	Remote Similarity	NPD4063	Clinical (unspecified phase)
0.6349	Remote Similarity	NPD5656	Clinical (unspecified phase)
0.6345	Remote Similarity	NPD518	Clinical (unspecified phase)
0.6345	Remote Similarity	NPD4478	Clinical (unspecified phase)
0.6335	Remote Similarity	NPD7606	Phase 3
0.6328	Remote Similarity	NPD7631	Approved
0.6319	Remote Similarity	NPD4416	Clinical (unspecified phase)
0.6312	Remote Similarity	NPD4942	Approved
0.6309	Remote Similarity	NPD1781	Discontinued
0.6309	Remote Similarity	NPD3626	Phase 3
0.6309	Remote Similarity	NPD7582	Discontinued
0.6308	Remote Similarity	NPD5963	Phase 2
0.6308	Remote Similarity	NPD5964	Phase 2
0.6308	Remote Similarity	NPD2895	Discontinued
0.6299	Remote Similarity	NPD3346	Approved
0.6299	Remote Similarity	NPD3344	Approved
0.6284	Remote Similarity	NPD3894	Discontinued
0.6282	Remote Similarity	NPD3434	Clinical (unspecified phase)
0.6279	Remote Similarity	NPD3982	Approved
0.6279	Remote Similarity	NPD6549	Approved
0.6279	Remote Similarity	NPD3980	Approved
0.6279	Remote Similarity	NPD4545	Approved
0.6279	Remote Similarity	NPD4542	Approved
0.6279	Remote Similarity	NPD6548	Approved
0.6276	Remote Similarity	NPD7457	Clinical (unspecified phase)
0.6276	Remote Similarity	NPD5576	Approved
0.6276	Remote Similarity	NPD5579	Approved
0.6275	Remote Similarity	NPD7733	Phase 2
0.6268	Remote Similarity	NPD1344	Phase 2
0.6268	Remote Similarity	NPD5162	Approved
0.6267	Remote Similarity	NPD5131	Approved
0.625	Remote Similarity	NPD7170	Discontinued
0.625	Remote Similarity	NPD1874	Clinical (unspecified phase)

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