NPASS Compound

Structure

CID178054 OpenBabel06191715552D 30 33 0 0 1 0 0 0 0 0999 V2000 0.8406 2.4265 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6811 2.9118 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6811 0.9706 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0433 1.9412 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2028 3.3971 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5217 -1.4559 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8406 -1.4559 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8406 1.4559 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0433 2.9118 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6811 -1.9412 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5217 2.4265 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5217 1.4559 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2028 1.4559 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3622 2.9118 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5217 -0.4853 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8406 -0.4853 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3622 1.9412 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6811 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6811 0.9706 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8406 1.4559 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.0000 0.9706 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.8839 3.3971 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.6811 -2.9118 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.3622 2.9118 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.3622 0.9706 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.2028 0.4853 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5217 3.3971 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.3622 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8406 2.4265 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 2 2 0 0 0 0 1 8 1 0 0 0 0 2 11 1 0 0 0 0 3 8 2 0 0 0 0 3 12 1 0 0 0 0 4 9 2 0 0 0 0 4 13 1 0 0 0 0 5 9 1 0 0 0 0 5 14 2 0 0 0 0 6 10 2 0 0 0 0 6 15 1 0 0 0 0 7 10 1 0 0 0 0 7 16 2 0 0 0 0 9 22 1 0 0 0 0 10 23 1 0 0 0 0 11 12 2 0 0 0 0 11 24 1 0 0 0 0 12 25 1 0 0 0 0 13 17 2 0 0 0 0 13 26 1 0 0 0 0 14 17 1 0 0 0 0 14 27 1 0 0 0 0 15 18 2 0 0 0 0 15 28 1 0 0 0 0 16 18 1 0 0 0 0 16 30 1 0 0 0 0 18 19 1 0 0 0 0 19 17 1 6 0 0 0 19 20 1 0 0 0 0 20 21 1 0 0 0 0 20 29 1 1 0 0 0 21 8 1 1 0 0 0 21 30 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	414.1
Volume:	392.93
LogP:	1.615
LogD:	1.381
LogS:	-3.769
# Rotatable Bonds:	2
TPSA:	171.07
# H-Bond Aceptor:	9
# H-Bond Donor:	8
# Rings:	4
# Heavy Atoms:	9

MedChem Properties

QED Drug-Likeness Score:	0.293
Synthetic Accessibility Score:	3.825
Fsp3:	0.143
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Accepted
Chelating Alert:	1
PAINS Alert:	1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.615
MDCK Permeability:	4.1702951421029866e-06
Pgp-inhibitor:	0.037
Pgp-substrate:	0.007
Human Intestinal Absorption (HIA):	0.831
20% Bioavailability (F20%):	0.999
30% Bioavailability (F30%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.009
Plasma Protein Binding (PPB):	89.93030548095703%
Volume Distribution (VD):	0.587
Pgp-substrate:	7.491124629974365%

ADMET: Metabolism

CYP1A2-inhibitor:	0.265
CYP1A2-substrate:	0.237
CYP2C19-inhibitor:	0.044
CYP2C19-substrate:	0.047
CYP2C9-inhibitor:	0.658
CYP2C9-substrate:	0.974
CYP2D6-inhibitor:	0.057
CYP2D6-substrate:	0.263
CYP3A4-inhibitor:	0.181
CYP3A4-substrate:	0.157

ADMET: Excretion

Clearance (CL):	13.543
Half-life (T1/2):	0.88

ADMET: Toxicity

hERG Blockers:	0.073
Human Hepatotoxicity (H-HT):	0.157
Drug-inuced Liver Injury (DILI):	0.847
AMES Toxicity:	0.465
Rat Oral Acute Toxicity:	0.34
Maximum Recommended Daily Dose:	0.892
Skin Sensitization:	0.958
Carcinogencity:	0.03
Eye Corrosion:	0.003
Eye Irritation:	0.92
Respiratory Toxicity:	0.076

Download Data

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

Natural Product: NPC178054

Natural Product ID:	NPC178054
*Common Name:**	(2R,3R,4S)-2-(3,4-Dihydroxyphenyl)-4-(2,4,6-Trihydroxyphenyl)Chroman-3,5,7-Triol
IUPAC Name:	(2R,3R,4S)-2-(3,4-dihydroxyphenyl)-4-(2,4,6-trihydroxyphenyl)-3,4-dihydro-2H-chromene-3,5,7-triol
Synonyms:
Standard InCHIKey:	OKJJBTUOKCQSPH-PWRODBHTSA-N
Standard InCHI:	InChI=1S/C21H18O9/c22-9-4-13(26)17(14(27)5-9)19-18-15(28)6-10(23)7-16(18)30-21(20(19)29)8-1-2-11(24)12(25)3-8/h1-7,19-29H/t19-,20+,21+/m0/s1
SMILES:	c1cc(c(cc1[C@@H]1[C@@H]([C@@H](c2c(cc(cc2O)O)O)c2c(cc(cc2O1)O)O)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL1223837
PubChem CID:	14009028
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0000337] Flavans [CHEMONTID:0003012] Flavan-3-ols [CHEMONTID:0001584] Catechins

*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
NPO23907	Grazielia serrata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8413	Echinus auritus	Species	Echinidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11409	Trichothecium sympodiale	Species	n.a.	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13209	Strychnos tomentosa	Species	Loganiaceae	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
Others	2

Activity Type	# Activity
Individual Protein	2

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT907	Individual Protein	Ribonuclease pancreatic	Homo sapiens	Ratio	=	0.7038	n.a.	PMID[549809]
NPT907	Individual Protein	Ribonuclease pancreatic	Homo sapiens	Kb	=	6.76	10'4/M	PMID[549809]

☑ 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 NPC178054 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	557
0.1-0.2	1739
0.2-0.3	4978
0.3-0.4	11765
0.4-0.5	5961
0.5-0.6	4145
0.6-0.7	6342
0.7-0.8	5514
0.8-0.85	945
0.85-0.9	587
0.9-0.95	144
0.95-1	20

Similarity Score	Similarity Level	Natural Product ID
0.9568	High Similarity	NPC202742
0.9568	High Similarity	NPC82917
0.9568	High Similarity	NPC18185
0.9568	High Similarity	NPC204770
0.9568	High Similarity	NPC70409
0.9568	High Similarity	NPC170103
0.9568	High Similarity	NPC236202
0.9568	High Similarity	NPC58190
0.9568	High Similarity	NPC263940
0.9568	High Similarity	NPC262911
0.9568	High Similarity	NPC108811
0.9568	High Similarity	NPC294558
0.95	High Similarity	NPC20757
0.95	High Similarity	NPC227516
0.9496	High Similarity	NPC96576
0.9493	High Similarity	NPC171932
0.9493	High Similarity	NPC28440
0.9485	High Similarity	NPC266197
0.9485	High Similarity	NPC291101
0.9478	High Similarity	NPC164787
0.9433	High Similarity	NPC211561
0.9416	High Similarity	NPC471389
0.9412	High Similarity	NPC22517
0.9407	High Similarity	NPC265433
0.9407	High Similarity	NPC270456
0.9407	High Similarity	NPC269091
0.9407	High Similarity	NPC162659
0.9407	High Similarity	NPC16435
0.9407	High Similarity	NPC248727
0.9407	High Similarity	NPC302701
0.9407	High Similarity	NPC306441
0.9398	High Similarity	NPC261619
0.9398	High Similarity	NPC185604
0.9398	High Similarity	NPC61477
0.9398	High Similarity	NPC78770
0.9398	High Similarity	NPC126029
0.9398	High Similarity	NPC219876
0.9398	High Similarity	NPC15658
0.9366	High Similarity	NPC477612
0.9357	High Similarity	NPC260397
0.9357	High Similarity	NPC317053
0.9357	High Similarity	NPC324492
0.9353	High Similarity	NPC304894
0.9353	High Similarity	NPC15659
0.9343	High Similarity	NPC22317
0.9343	High Similarity	NPC262189
0.9343	High Similarity	NPC309124
0.9343	High Similarity	NPC184797
0.9338	High Similarity	NPC211549
0.9338	High Similarity	NPC474390
0.9333	High Similarity	NPC260898
0.9333	High Similarity	NPC234333
0.9333	High Similarity	NPC121812
0.9333	High Similarity	NPC112939
0.9333	High Similarity	NPC61946
0.9333	High Similarity	NPC47398
0.9333	High Similarity	NPC470356
0.9333	High Similarity	NPC151224
0.9333	High Similarity	NPC112246
0.9333	High Similarity	NPC94750
0.9333	High Similarity	NPC474206
0.9328	High Similarity	NPC11060
0.9323	High Similarity	NPC268266
0.9323	High Similarity	NPC268342
0.9323	High Similarity	NPC220825
0.9323	High Similarity	NPC42760
0.9291	High Similarity	NPC328567
0.9291	High Similarity	NPC320671
0.9291	High Similarity	NPC327412
0.9291	High Similarity	NPC320970
0.9281	High Similarity	NPC163508
0.9281	High Similarity	NPC173203
0.927	High Similarity	NPC245207
0.927	High Similarity	NPC471388
0.927	High Similarity	NPC70682
0.927	High Similarity	NPC236306
0.927	High Similarity	NPC473739
0.927	High Similarity	NPC232164
0.927	High Similarity	NPC127218
0.927	High Similarity	NPC319647
0.927	High Similarity	NPC260741
0.927	High Similarity	NPC25966
0.9265	High Similarity	NPC227503
0.9265	High Similarity	NPC470802
0.9265	High Similarity	NPC234952
0.9265	High Similarity	NPC474639
0.9265	High Similarity	NPC230734
0.9259	High Similarity	NPC317380
0.9259	High Similarity	NPC478085
0.9259	High Similarity	NPC170694
0.9236	High Similarity	NPC322899
0.9236	High Similarity	NPC469944
0.9236	High Similarity	NPC226809
0.9236	High Similarity	NPC226108
0.9236	High Similarity	NPC46283
0.9236	High Similarity	NPC134911
0.9236	High Similarity	NPC44192
0.9236	High Similarity	NPC272552
0.9236	High Similarity	NPC279406
0.9225	High Similarity	NPC329836
0.922	High Similarity	NPC268515
0.922	High Similarity	NPC40222
0.9214	High Similarity	NPC470097
0.9214	High Similarity	NPC469313
0.9214	High Similarity	NPC138227
0.9214	High Similarity	NPC168579
0.9214	High Similarity	NPC76176
0.9214	High Similarity	NPC114119
0.9214	High Similarity	NPC471415
0.9214	High Similarity	NPC473108
0.9209	High Similarity	NPC2613
0.9209	High Similarity	NPC107161
0.9209	High Similarity	NPC59841
0.9209	High Similarity	NPC475891
0.9209	High Similarity	NPC204347
0.9203	High Similarity	NPC55793
0.9197	High Similarity	NPC103976
0.9197	High Similarity	NPC474282
0.9197	High Similarity	NPC276490
0.9197	High Similarity	NPC326797
0.9197	High Similarity	NPC176051
0.9197	High Similarity	NPC102904
0.9197	High Similarity	NPC107551
0.9191	High Similarity	NPC473413
0.9185	High Similarity	NPC475840
0.9185	High Similarity	NPC263064
0.9172	High Similarity	NPC20050
0.9172	High Similarity	NPC224161
0.9172	High Similarity	NPC306267
0.9167	High Similarity	NPC321972
0.9167	High Similarity	NPC329343
0.9167	High Similarity	NPC324517
0.9149	High Similarity	NPC181615
0.9143	High Similarity	NPC37793
0.9137	High Similarity	NPC311530
0.9137	High Similarity	NPC247291
0.9137	High Similarity	NPC87725
0.9137	High Similarity	NPC277331
0.9137	High Similarity	NPC100482
0.9137	High Similarity	NPC263261
0.9137	High Similarity	NPC35216
0.913	High Similarity	NPC32630
0.9124	High Similarity	NPC472336
0.9124	High Similarity	NPC173660
0.9124	High Similarity	NPC472334
0.9118	High Similarity	NPC256307
0.9118	High Similarity	NPC66840
0.9111	High Similarity	NPC470752
0.9111	High Similarity	NPC160991
0.9111	High Similarity	NPC16208
0.9111	High Similarity	NPC202762
0.9111	High Similarity	NPC127624
0.9111	High Similarity	NPC184447
0.9111	High Similarity	NPC7903
0.9111	High Similarity	NPC86655
0.9111	High Similarity	NPC201587
0.9111	High Similarity	NPC35932
0.9111	High Similarity	NPC253105
0.911	High Similarity	NPC46335
0.9098	High Similarity	NPC226331
0.9098	High Similarity	NPC46274
0.9091	High Similarity	NPC281549
0.9085	High Similarity	NPC99515
0.9085	High Similarity	NPC125755
0.9085	High Similarity	NPC190714
0.9078	High Similarity	NPC93323
0.9078	High Similarity	NPC12641
0.9078	High Similarity	NPC280092
0.9078	High Similarity	NPC45257
0.9065	High Similarity	NPC27495
0.9065	High Similarity	NPC259519
0.9065	High Similarity	NPC160283
0.9065	High Similarity	NPC254759
0.9051	High Similarity	NPC195022
0.9051	High Similarity	NPC472337
0.9044	High Similarity	NPC168059
0.9044	High Similarity	NPC229442
0.9041	High Similarity	NPC78809
0.9037	High Similarity	NPC474017
0.9037	High Similarity	NPC472597
0.9037	High Similarity	NPC309787
0.9034	High Similarity	NPC2745
0.9028	High Similarity	NPC476969
0.9028	High Similarity	NPC470826
0.9028	High Similarity	NPC470098
0.9028	High Similarity	NPC318373
0.9028	High Similarity	NPC321657
0.9028	High Similarity	NPC473266
0.9023	High Similarity	NPC250432
0.9023	High Similarity	NPC5447
0.9021	High Similarity	NPC101376
0.9021	High Similarity	NPC474397
0.9021	High Similarity	NPC21776
0.9021	High Similarity	NPC16269
0.9021	High Similarity	NPC473480
0.9021	High Similarity	NPC15538
0.9014	High Similarity	NPC277867
0.9014	High Similarity	NPC472457
0.9014	High Similarity	NPC161700
0.9014	High Similarity	NPC475096

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 NPC178054 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	469
0.1-0.2	842
0.2-0.3	2034
0.3-0.4	2649
0.4-0.5	1547
0.5-0.6	870
0.6-0.7	598
0.7-0.8	128
0.8-0.85	7
0.85-0.9	4
0.9-0.95	0
0.95-1	2

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.9398	High Similarity	NPD1613	Approved
0.9398	High Similarity	NPD1612	Clinical (unspecified phase)
0.9098	High Similarity	NPD1529	Clinical (unspecified phase)
0.9023	High Similarity	NPD1530	Clinical (unspecified phase)
0.8955	High Similarity	NPD4908	Phase 1
0.8889	High Similarity	NPD3027	Phase 3
0.8824	High Similarity	NPD4907	Clinical (unspecified phase)
0.8571	High Similarity	NPD1610	Phase 2
0.8487	Intermediate Similarity	NPD4868	Clinical (unspecified phase)
0.8344	Intermediate Similarity	NPD6167	Clinical (unspecified phase)
0.8344	Intermediate Similarity	NPD6168	Clinical (unspecified phase)
0.8344	Intermediate Similarity	NPD6166	Phase 2
0.8333	Intermediate Similarity	NPD2861	Phase 2
0.817	Intermediate Similarity	NPD1934	Approved
0.8146	Intermediate Similarity	NPD1653	Approved
0.8134	Intermediate Similarity	NPD1548	Phase 1
0.8117	Intermediate Similarity	NPD2393	Clinical (unspecified phase)
0.8043	Intermediate Similarity	NPD4749	Approved
0.8028	Intermediate Similarity	NPD6410	Clinical (unspecified phase)
0.7975	Intermediate Similarity	NPD7993	Clinical (unspecified phase)
0.7973	Intermediate Similarity	NPD6674	Discontinued
0.7958	Intermediate Similarity	NPD4625	Phase 3
0.7925	Intermediate Similarity	NPD7199	Phase 2
0.7914	Intermediate Similarity	NPD7074	Phase 3
0.7911	Intermediate Similarity	NPD6234	Discontinued
0.7901	Intermediate Similarity	NPD7228	Approved
0.7853	Intermediate Similarity	NPD7054	Approved
0.7853	Intermediate Similarity	NPD5844	Phase 1
0.7852	Intermediate Similarity	NPD5698	Clinical (unspecified phase)
0.7821	Intermediate Similarity	NPD37	Approved
0.7817	Intermediate Similarity	NPD3018	Phase 2
0.7806	Intermediate Similarity	NPD4380	Phase 2
0.7805	Intermediate Similarity	NPD7472	Approved
0.7791	Intermediate Similarity	NPD3818	Discontinued
0.7785	Intermediate Similarity	NPD4965	Approved
0.7785	Intermediate Similarity	NPD4967	Phase 2
0.7785	Intermediate Similarity	NPD4966	Approved
0.7771	Intermediate Similarity	NPD2801	Approved
0.777	Intermediate Similarity	NPD1091	Approved
0.7763	Intermediate Similarity	NPD7213	Phase 3
0.7763	Intermediate Similarity	NPD1511	Approved
0.7763	Intermediate Similarity	NPD7212	Phase 2
0.7758	Intermediate Similarity	NPD6797	Phase 2
0.7736	Intermediate Similarity	NPD4381	Clinical (unspecified phase)
0.7722	Intermediate Similarity	NPD8443	Clinical (unspecified phase)
0.7718	Intermediate Similarity	NPD7266	Discontinued
0.7716	Intermediate Similarity	NPD7184	Clinical (unspecified phase)
0.7712	Intermediate Similarity	NPD7004	Clinical (unspecified phase)
0.7712	Intermediate Similarity	NPD7447	Phase 1
0.7711	Intermediate Similarity	NPD7251	Discontinued
0.7671	Intermediate Similarity	NPD4060	Phase 1
0.7671	Intermediate Similarity	NPD3619	Clinical (unspecified phase)
0.7671	Intermediate Similarity	NPD3620	Phase 2
0.7665	Intermediate Similarity	NPD4338	Clinical (unspecified phase)
0.7662	Intermediate Similarity	NPD1512	Approved
0.766	Intermediate Similarity	NPD2983	Phase 2
0.766	Intermediate Similarity	NPD2982	Phase 2
0.7658	Intermediate Similarity	NPD1465	Phase 2
0.763	Intermediate Similarity	NPD5283	Phase 1
0.7619	Intermediate Similarity	NPD5124	Phase 1
0.7619	Intermediate Similarity	NPD5123	Clinical (unspecified phase)
0.76	Intermediate Similarity	NPD2029	Clinical (unspecified phase)
0.7589	Intermediate Similarity	NPD2981	Phase 2
0.7562	Intermediate Similarity	NPD3882	Suspended
0.756	Intermediate Similarity	NPD7808	Phase 3
0.756	Intermediate Similarity	NPD7549	Discontinued
0.7547	Intermediate Similarity	NPD8455	Phase 2
0.7531	Intermediate Similarity	NPD5494	Approved
0.7518	Intermediate Similarity	NPD7157	Approved
0.7517	Intermediate Similarity	NPD4537	Clinical (unspecified phase)
0.7517	Intermediate Similarity	NPD4538	Approved
0.7517	Intermediate Similarity	NPD4536	Approved
0.75	Intermediate Similarity	NPD5846	Approved
0.75	Intermediate Similarity	NPD6516	Phase 2
0.75	Intermediate Similarity	NPD3817	Phase 2
0.75	Intermediate Similarity	NPD6917	Clinical (unspecified phase)
0.75	Intermediate Similarity	NPD1652	Phase 2
0.7485	Intermediate Similarity	NPD6959	Discontinued
0.7484	Intermediate Similarity	NPD4160	Clinical (unspecified phase)
0.7483	Intermediate Similarity	NPD8651	Approved
0.7483	Intermediate Similarity	NPD1550	Clinical (unspecified phase)
0.7483	Intermediate Similarity	NPD1552	Clinical (unspecified phase)
0.7481	Intermediate Similarity	NPD228	Approved
0.7471	Intermediate Similarity	NPD8053	Approved
0.7471	Intermediate Similarity	NPD8054	Approved
0.7467	Intermediate Similarity	NPD5588	Approved
0.7467	Intermediate Similarity	NPD5960	Phase 3
0.7463	Intermediate Similarity	NPD3022	Approved
0.7463	Intermediate Similarity	NPD3021	Approved
0.7451	Intermediate Similarity	NPD7466	Approved
0.7451	Intermediate Similarity	NPD3892	Phase 2
0.7439	Intermediate Similarity	NPD6232	Discontinued
0.7439	Intermediate Similarity	NPD3787	Discontinued
0.7434	Intermediate Similarity	NPD1549	Phase 2
0.7426	Intermediate Similarity	NPD7843	Approved
0.7417	Intermediate Similarity	NPD6100	Approved
0.7417	Intermediate Similarity	NPD6099	Approved
0.7415	Intermediate Similarity	NPD6859	Clinical (unspecified phase)
0.7415	Intermediate Similarity	NPD6798	Discontinued
0.741	Intermediate Similarity	NPD7473	Discontinued
0.7407	Intermediate Similarity	NPD7975	Clinical (unspecified phase)
0.7407	Intermediate Similarity	NPD7075	Discontinued
0.7403	Intermediate Similarity	NPD6190	Approved
0.7396	Intermediate Similarity	NPD6559	Discontinued
0.7396	Intermediate Similarity	NPD7240	Approved
0.7391	Intermediate Similarity	NPD6671	Approved
0.7391	Intermediate Similarity	NPD5402	Approved
0.7388	Intermediate Similarity	NPD2684	Approved
0.7386	Intermediate Similarity	NPD5177	Phase 3
0.7384	Intermediate Similarity	NPD4663	Approved
0.7383	Intermediate Similarity	NPD5735	Approved
0.7379	Intermediate Similarity	NPD6584	Phase 3
0.7351	Intermediate Similarity	NPD6029	Clinical (unspecified phase)
0.7351	Intermediate Similarity	NPD6028	Clinical (unspecified phase)
0.7338	Intermediate Similarity	NPD3750	Approved
0.7321	Intermediate Similarity	NPD7804	Clinical (unspecified phase)
0.7315	Intermediate Similarity	NPD1558	Phase 1
0.7313	Intermediate Similarity	NPD290	Approved
0.7312	Intermediate Similarity	NPD7411	Suspended
0.731	Intermediate Similarity	NPD4577	Approved
0.731	Intermediate Similarity	NPD4578	Approved
0.7292	Intermediate Similarity	NPD4379	Clinical (unspecified phase)
0.7292	Intermediate Similarity	NPD3600	Clinical (unspecified phase)
0.729	Intermediate Similarity	NPD5307	Clinical (unspecified phase)
0.729	Intermediate Similarity	NPD2677	Approved
0.7285	Intermediate Similarity	NPD7097	Phase 1
0.7284	Intermediate Similarity	NPD6374	Clinical (unspecified phase)
0.7278	Intermediate Similarity	NPD5403	Approved
0.7273	Intermediate Similarity	NPD422	Phase 1
0.7267	Intermediate Similarity	NPD6355	Discontinued
0.7262	Intermediate Similarity	NPD3751	Discontinued
0.7261	Intermediate Similarity	NPD7410	Clinical (unspecified phase)
0.7261	Intermediate Similarity	NPD4378	Clinical (unspecified phase)
0.7255	Intermediate Similarity	NPD3540	Phase 1
0.7255	Intermediate Similarity	NPD5762	Approved
0.7255	Intermediate Similarity	NPD5763	Approved
0.725	Intermediate Similarity	NPD4678	Approved
0.725	Intermediate Similarity	NPD4675	Approved
0.7248	Intermediate Similarity	NPD6233	Phase 2
0.7246	Intermediate Similarity	NPD2489	Approved
0.7246	Intermediate Similarity	NPD27	Approved
0.7244	Intermediate Similarity	NPD5058	Phase 3
0.7241	Intermediate Similarity	NPD7906	Approved
0.7239	Intermediate Similarity	NPD7768	Phase 2
0.723	Intermediate Similarity	NPD7095	Approved
0.7229	Intermediate Similarity	NPD3051	Approved
0.7226	Intermediate Similarity	NPD6398	Clinical (unspecified phase)
0.7225	Intermediate Similarity	NPD8055	Clinical (unspecified phase)
0.7222	Intermediate Similarity	NPD7819	Suspended
0.7222	Intermediate Similarity	NPD7096	Clinical (unspecified phase)
0.7205	Intermediate Similarity	NPD7615	Clinical (unspecified phase)
0.72	Intermediate Similarity	NPD5837	Clinical (unspecified phase)
0.72	Intermediate Similarity	NPD2238	Phase 2
0.7197	Intermediate Similarity	NPD7041	Phase 2
0.7197	Intermediate Similarity	NPD7040	Clinical (unspecified phase)
0.719	Intermediate Similarity	NPD3539	Phase 1
0.7188	Intermediate Similarity	NPD4005	Discontinued
0.7188	Intermediate Similarity	NPD5808	Clinical (unspecified phase)
0.7188	Intermediate Similarity	NPD6055	Clinical (unspecified phase)
0.7186	Intermediate Similarity	NPD2970	Approved
0.7186	Intermediate Similarity	NPD2969	Approved
0.7172	Intermediate Similarity	NPD6583	Phase 3
0.7172	Intermediate Similarity	NPD6582	Phase 2
0.7169	Intermediate Similarity	NPD8127	Discontinued
0.716	Intermediate Similarity	NPD6801	Discontinued
0.7153	Intermediate Similarity	NPD3705	Approved
0.7152	Intermediate Similarity	NPD5401	Approved
0.7143	Intermediate Similarity	NPD7852	Clinical (unspecified phase)
0.7126	Intermediate Similarity	NPD7229	Phase 3
0.7124	Intermediate Similarity	NPD1510	Phase 2
0.7118	Intermediate Similarity	NPD8156	Discontinued
0.7117	Intermediate Similarity	NPD6818	Clinical (unspecified phase)
0.7115	Intermediate Similarity	NPD4628	Phase 3
0.7115	Intermediate Similarity	NPD6331	Phase 2
0.7111	Intermediate Similarity	NPD968	Approved
0.711	Intermediate Similarity	NPD7313	Approved
0.711	Intermediate Similarity	NPD7310	Approved
0.711	Intermediate Similarity	NPD7311	Approved
0.711	Intermediate Similarity	NPD8312	Approved
0.711	Intermediate Similarity	NPD8313	Approved
0.711	Intermediate Similarity	NPD7312	Approved
0.7107	Intermediate Similarity	NPD1940	Clinical (unspecified phase)
0.7104	Intermediate Similarity	NPD7680	Approved
0.7103	Intermediate Similarity	NPD2235	Phase 2
0.7103	Intermediate Similarity	NPD2231	Phase 2
0.7097	Intermediate Similarity	NPD7037	Approved
0.7097	Intermediate Similarity	NPD2424	Discontinued
0.7089	Intermediate Similarity	NPD6143	Clinical (unspecified phase)
0.7086	Intermediate Similarity	NPD4140	Approved
0.708	Intermediate Similarity	NPD4750	Phase 3
0.7078	Intermediate Similarity	NPD2796	Approved
0.7075	Intermediate Similarity	NPD3094	Phase 2
0.7072	Intermediate Similarity	NPD7237	Clinical (unspecified phase)
0.7069	Intermediate Similarity	NPD7309	Approved
0.7063	Intermediate Similarity	NPD6980	Clinical (unspecified phase)
0.7059	Intermediate Similarity	NPD8252	Approved
0.7059	Intermediate Similarity	NPD8251	Approved
0.7059	Intermediate Similarity	NPD8099	Discontinued
0.7055	Intermediate Similarity	NPD5327	Phase 3
0.7051	Intermediate Similarity	NPD3060	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