NPASS Compound

Structure

CID3642 OpenBabel06191715322D 36 40 0 0 1 0 0 0 0 0999 V2000 2.5981 3.5000 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 -2.5981 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -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 4.3301 0.5000 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 6.0622 1.5000 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 3.4641 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 2.0000 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 -0.8660 -1.5000 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 -0.8660 1.5000 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 5.1962 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 2.0000 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 -0.0000 -1.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.7321 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 2.0000 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 3.0000 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 2.5981 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -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 35 1 0 0 0 0 2 3 2 0 0 0 0 2 4 1 0 0 0 0 3 9 1 0 0 0 0 4 10 2 0 0 0 0 5 7 2 0 0 0 0 5 11 1 0 0 0 0 6 8 2 0 0 0 0 6 12 1 0 0 0 0 7 13 1 0 0 0 0 8 14 1 0 0 0 0 9 18 2 0 0 0 0 10 18 1 0 0 0 0 11 19 2 0 0 0 0 12 20 2 0 0 0 0 13 23 2 0 0 0 0 14 24 2 0 0 0 0 15 19 1 0 0 0 0 15 21 1 0 0 0 0 16 20 1 0 0 0 0 16 22 1 0 0 0 0 17 25 1 0 0 0 0 17 26 1 0 0 0 0 19 23 1 0 0 0 0 20 24 1 0 0 0 0 21 28 2 0 0 0 0 21 29 1 0 0 0 0 22 29 2 0 0 0 0 22 30 1 0 0 0 0 23 31 1 0 0 0 0 24 32 1 0 0 0 0 25 27 1 0 0 0 0 25 33 2 0 0 0 0 26 18 1 1 0 0 0 26 36 1 0 0 0 0 27 28 1 0 0 0 0 27 30 2 0 0 0 0 28 34 1 0 0 0 0 29 35 1 0 0 0 0 30 36 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	482.17
Volume:	503.121
LogP:	5.915
LogD:	3.688
LogS:	-4.002
# Rotatable Bonds:	6
TPSA:	96.22
# H-Bond Aceptor:	6
# H-Bond Donor:	3
# Rings:	5
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.326
Synthetic Accessibility Score:	3.234
Fsp3:	0.167
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.123
MDCK Permeability:	2.929638503701426e-05
Pgp-inhibitor:	0.121
Pgp-substrate:	0.002
Human Intestinal Absorption (HIA):	0.006
20% Bioavailability (F20%):	0.116
30% Bioavailability (F30%):	0.869

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.032
Plasma Protein Binding (PPB):	100.40428161621094%
Volume Distribution (VD):	0.41
Pgp-substrate:	0.9634755849838257%

ADMET: Metabolism

CYP1A2-inhibitor:	0.181
CYP1A2-substrate:	0.614
CYP2C19-inhibitor:	0.961
CYP2C19-substrate:	0.09
CYP2C9-inhibitor:	0.887
CYP2C9-substrate:	0.975
CYP2D6-inhibitor:	0.186
CYP2D6-substrate:	0.687
CYP3A4-inhibitor:	0.457
CYP3A4-substrate:	0.6

ADMET: Excretion

Clearance (CL):	10.768
Half-life (T1/2):	0.339

ADMET: Toxicity

hERG Blockers:	0.033
Human Hepatotoxicity (H-HT):	0.128
Drug-inuced Liver Injury (DILI):	0.966
AMES Toxicity:	0.052
Rat Oral Acute Toxicity:	0.88
Maximum Recommended Daily Dose:	0.05
Skin Sensitization:	0.936
Carcinogencity:	0.181
Eye Corrosion:	0.003
Eye Irritation:	0.9
Respiratory Toxicity:	0.311

Download Data

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

Natural Product: NPC3642

Natural Product ID:	NPC3642
*Common Name:**	7-Methoxydichamanetin
IUPAC Name:	(2S)-5-hydroxy-6,8-bis[(2-hydroxyphenyl)methyl]-7-methoxy-2-phenyl-2,3-dihydrochromen-4-one
Synonyms:	7-Methoxydichamanetin
Standard InCHIKey:	HUNWUDHAPSHKOD-SANMLTNESA-N
Standard InCHI:	InChI=1S/C30H26O6/c1-35-29-21(15-19-11-5-7-13-23(19)31)28(34)27-25(33)17-26(18-9-3-2-4-10-18)36-30(27)22(29)16-20-12-6-8-14-24(20)32/h2-14,26,31-32,34H,15-17H2,1H3/t26-/m0/s1
SMILES:	COc1c(Cc2ccccc2O)c2O[C@@H](CC(=O)c2c(c1Cc1ccccc1O)O)c1ccccc1
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL1835969
PubChem CID:	56656188
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0002650] Diarylheptanoids [CHEMONTID:0002651] Linear diarylheptanoids

*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
NPO3803	Ardisia japonica	Species	Primulaceae	Eukaryota	whole plants	Sendai, Miyagi Prefecture, Japan	2000-Sep	PMID[17243725]
NPO3803	Ardisia japonica	Species	Primulaceae	Eukaryota	n.a.	whole plant	n.a.	PMID[17243725]
NPO3803	Ardisia japonica	Species	Primulaceae	Eukaryota	n.a.	whole plant	n.a.	PMID[17397219]
NPO2846	Piper sarmentosum	Species	Piperaceae	Eukaryota	n.a.	leaf	n.a.	PMID[21973101]
NPO2846	Piper sarmentosum	Species	Piperaceae	Eukaryota	n.a.	inflorescence	n.a.	PMID[21973101]
NPO2846	Piper sarmentosum	Species	Piperaceae	Eukaryota	n.a.	Kego Nature Reserve, Hatinh Province, Vietnam	2008-DEC	PMID[21973101]
NPO2846	Piper sarmentosum	Species	Piperaceae	Eukaryota	n.a.	twig	n.a.	PMID[21973101]
NPO2846	Piper sarmentosum	Species	Piperaceae	Eukaryota	aerial parts	Kego Nature Reserve, Hatinh Province, Vietnam	2008-DEC	PMID[21973101]
NPO2846	Piper sarmentosum	Species	Piperaceae	Eukaryota	n.a.	stem	n.a.	PMID[21973101]
NPO3803	Ardisia japonica	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[22940450]
NPO4720	Aglaia perviridis	Species	Meliaceae	Eukaryota	leaves, twigs, and fruits	Nui Chua National Park (11 43' N; 109 08' E; 730 m alt.), Ninh Thuan Province, Vietnam	2010-Jan	PMID[23301897]
NPO4720	Aglaia perviridis	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[31621322]
NPO3803	Ardisia japonica	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO2846	Piper sarmentosum	Species	Piperaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO2846	Piper sarmentosum	Species	Piperaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3803	Ardisia japonica	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3803	Ardisia japonica	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO3803	Ardisia japonica	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO5657	Oocystis polymorpha	Species	Oocystaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4720	Aglaia perviridis	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3803	Ardisia japonica	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6614	Rubus pileatus	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1912	Acanthosyris paulo-alvinii	Species	Cervantesiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO61	Phoebe grandis	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO992	Betula alnoides	Species	Betulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2846	Piper sarmentosum	Species	Piperaceae	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	3

Activity Type	# Activity
Cell Line	2
Others	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT139	Cell Line	HT-29	Homo sapiens	ED50	>	20.0	uM	PMID[490786]
NPT139	Cell Line	HT-29	Homo sapiens	ED50	=	1.6	uM	PMID[490786]
NPT2	Others	Unspecified		ED50	=	3.45	uM	PMID[490786]

☑ 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 NPC3642 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	383
0.1-0.2	1662
0.2-0.3	4080
0.3-0.4	10870
0.4-0.5	7420
0.5-0.6	3917
0.6-0.7	5836
0.7-0.8	5026
0.8-0.85	2111
0.85-0.9	915
0.9-0.95	421
0.95-1	56

Similarity Score	Similarity Level	Natural Product ID
0.993	High Similarity	NPC122894
0.9789	High Similarity	NPC109183
0.9789	High Similarity	NPC473078
0.9789	High Similarity	NPC470133
0.9789	High Similarity	NPC470132
0.9789	High Similarity	NPC470131
0.9789	High Similarity	NPC470134
0.9718	High Similarity	NPC470135
0.9718	High Similarity	NPC470136
0.9718	High Similarity	NPC39045
0.9658	High Similarity	NPC115601
0.9658	High Similarity	NPC39154
0.9658	High Similarity	NPC208011
0.9658	High Similarity	NPC174086
0.9658	High Similarity	NPC78324
0.965	High Similarity	NPC228779
0.9592	High Similarity	NPC121568
0.9586	High Similarity	NPC132345
0.9577	High Similarity	NPC177354
0.9577	High Similarity	NPC64915
0.9577	High Similarity	NPC76338
0.9577	High Similarity	NPC167624
0.9577	High Similarity	NPC324436
0.9577	High Similarity	NPC220998
0.9577	High Similarity	NPC66515
0.9577	High Similarity	NPC37496
0.9577	High Similarity	NPC10937
0.9577	High Similarity	NPC194432
0.9577	High Similarity	NPC40833
0.9577	High Similarity	NPC328164
0.9577	High Similarity	NPC148757
0.9577	High Similarity	NPC125855
0.9577	High Similarity	NPC324134
0.9577	High Similarity	NPC296917
0.9577	High Similarity	NPC1089
0.9577	High Similarity	NPC161506
0.9577	High Similarity	NPC306829
0.9577	High Similarity	NPC182852
0.9577	High Similarity	NPC166934
0.9577	High Similarity	NPC76372
0.9577	High Similarity	NPC228504
0.9577	High Similarity	NPC32739
0.9577	High Similarity	NPC265040
0.9577	High Similarity	NPC107572
0.9577	High Similarity	NPC227579
0.9577	High Similarity	NPC78
0.9577	High Similarity	NPC166482
0.9577	High Similarity	NPC223500
0.953	High Similarity	NPC1796
0.953	High Similarity	NPC475184
0.953	High Similarity	NPC257166
0.9527	High Similarity	NPC66441
0.9527	High Similarity	NPC182555
0.9527	High Similarity	NPC134171
0.9527	High Similarity	NPC300668
0.9517	High Similarity	NPC161191
0.9514	High Similarity	NPC267375
0.9514	High Similarity	NPC88964
0.9514	High Similarity	NPC312973
0.9514	High Similarity	NPC20488
0.9514	High Similarity	NPC67805
0.9514	High Similarity	NPC111786
0.9514	High Similarity	NPC470647
0.9514	High Similarity	NPC54577
0.9514	High Similarity	NPC83357
0.9514	High Similarity	NPC301276
0.9514	High Similarity	NPC475052
0.9514	High Similarity	NPC176229
0.9514	High Similarity	NPC142405
0.9514	High Similarity	NPC214774
0.9514	High Similarity	NPC246948
0.9514	High Similarity	NPC195621
0.951	High Similarity	NPC257097
0.951	High Similarity	NPC278249
0.951	High Similarity	NPC125894
0.951	High Similarity	NPC214166
0.951	High Similarity	NPC164980
0.951	High Similarity	NPC185276
0.951	High Similarity	NPC81697
0.951	High Similarity	NPC77794
0.951	High Similarity	NPC478086
0.951	High Similarity	NPC143896
0.951	High Similarity	NPC150408
0.951	High Similarity	NPC68104
0.951	High Similarity	NPC85162
0.951	High Similarity	NPC39329
0.951	High Similarity	NPC169591
0.951	High Similarity	NPC149026
0.951	High Similarity	NPC221432
0.951	High Similarity	NPC175504
0.951	High Similarity	NPC91560
0.951	High Similarity	NPC310130
0.951	High Similarity	NPC75049
0.951	High Similarity	NPC223812
0.951	High Similarity	NPC316816
0.951	High Similarity	NPC107177
0.9507	High Similarity	NPC166689
0.9507	High Similarity	NPC110038
0.9507	High Similarity	NPC17170
0.9507	High Similarity	NPC258630
0.9507	High Similarity	NPC96408
0.9507	High Similarity	NPC26238
0.9507	High Similarity	NPC324386
0.9507	High Similarity	NPC156190
0.9507	High Similarity	NPC4743
0.9507	High Similarity	NPC312391
0.9507	High Similarity	NPC213322
0.9507	High Similarity	NPC248372
0.9507	High Similarity	NPC279650
0.9467	High Similarity	NPC15815
0.9467	High Similarity	NPC51247
0.9467	High Similarity	NPC51760
0.9467	High Similarity	NPC105584
0.9463	High Similarity	NPC69531
0.9463	High Similarity	NPC32867
0.9456	High Similarity	NPC178484
0.9448	High Similarity	NPC23728
0.9448	High Similarity	NPC283234
0.9448	High Similarity	NPC110303
0.9448	High Similarity	NPC296998
0.9448	High Similarity	NPC473077
0.9444	High Similarity	NPC131568
0.9444	High Similarity	NPC131579
0.9444	High Similarity	NPC473014
0.9444	High Similarity	NPC319752
0.9444	High Similarity	NPC236766
0.9444	High Similarity	NPC235217
0.9444	High Similarity	NPC197252
0.9444	High Similarity	NPC473013
0.9444	High Similarity	NPC209040
0.9444	High Similarity	NPC473015
0.9437	High Similarity	NPC6407
0.9437	High Similarity	NPC110228
0.9437	High Similarity	NPC188243
0.9404	High Similarity	NPC42965
0.9404	High Similarity	NPC98023
0.9404	High Similarity	NPC226462
0.9404	High Similarity	NPC195136
0.9396	High Similarity	NPC79375
0.9396	High Similarity	NPC37253
0.9384	High Similarity	NPC160821
0.9384	High Similarity	NPC321623
0.9384	High Similarity	NPC132592
0.9384	High Similarity	NPC189087
0.9379	High Similarity	NPC127059
0.9379	High Similarity	NPC474161
0.9379	High Similarity	NPC476088
0.9379	High Similarity	NPC472629
0.9379	High Similarity	NPC285630
0.9371	High Similarity	NPC14871
0.9371	High Similarity	NPC3188
0.9366	High Similarity	NPC310135
0.9366	High Similarity	NPC222342
0.9366	High Similarity	NPC150648
0.9366	High Similarity	NPC225153
0.9366	High Similarity	NPC274784
0.9366	High Similarity	NPC329203
0.9366	High Similarity	NPC20709
0.9366	High Similarity	NPC265871
0.9366	High Similarity	NPC140890
0.9342	High Similarity	NPC312273
0.9342	High Similarity	NPC301256
0.9338	High Similarity	NPC295090
0.9338	High Similarity	NPC123544
0.9333	High Similarity	NPC198489
0.9333	High Similarity	NPC61112
0.9329	High Similarity	NPC303485
0.9329	High Similarity	NPC290830
0.9329	High Similarity	NPC71061
0.9329	High Similarity	NPC194593
0.9329	High Similarity	NPC72425
0.9324	High Similarity	NPC78835
0.9324	High Similarity	NPC204561
0.9324	High Similarity	NPC317715
0.9324	High Similarity	NPC316960
0.9324	High Similarity	NPC309512
0.9324	High Similarity	NPC148945
0.9324	High Similarity	NPC325429
0.932	High Similarity	NPC291746
0.932	High Similarity	NPC288840
0.932	High Similarity	NPC473016
0.9315	High Similarity	NPC10990
0.9315	High Similarity	NPC300988
0.9315	High Similarity	NPC472627
0.931	High Similarity	NPC87486
0.931	High Similarity	NPC470890
0.931	High Similarity	NPC124780
0.931	High Similarity	NPC194949
0.931	High Similarity	NPC271288
0.931	High Similarity	NPC282957
0.9306	High Similarity	NPC147145
0.9301	High Similarity	NPC159275
0.9301	High Similarity	NPC69769
0.9301	High Similarity	NPC241100
0.9301	High Similarity	NPC76445
0.9301	High Similarity	NPC284550
0.9301	High Similarity	NPC129853
0.9296	High Similarity	NPC243528
0.9296	High Similarity	NPC251681
0.9281	High Similarity	NPC473012

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 NPC3642 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	350
0.1-0.2	967
0.2-0.3	1524
0.3-0.4	2671
0.4-0.5	1868
0.5-0.6	1169
0.6-0.7	407
0.7-0.8	145
0.8-0.85	25
0.85-0.9	18
0.9-0.95	6
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.9267	High Similarity	NPD8443	Clinical (unspecified phase)
0.9225	High Similarity	NPD1550	Clinical (unspecified phase)
0.9225	High Similarity	NPD1552	Clinical (unspecified phase)
0.9195	High Similarity	NPD7411	Suspended
0.9178	High Similarity	NPD7410	Clinical (unspecified phase)
0.9161	High Similarity	NPD1549	Phase 2
0.9091	High Similarity	NPD6959	Discontinued
0.9048	High Similarity	NPD4378	Clinical (unspecified phase)
0.9038	High Similarity	NPD7852	Clinical (unspecified phase)
0.8947	High Similarity	NPD2393	Clinical (unspecified phase)
0.8874	High Similarity	NPD4380	Phase 2
0.8831	High Similarity	NPD7768	Phase 2
0.8774	High Similarity	NPD7075	Discontinued
0.8759	High Similarity	NPD2796	Approved
0.8701	High Similarity	NPD7096	Clinical (unspecified phase)
0.869	High Similarity	NPD1510	Phase 2
0.8679	High Similarity	NPD6167	Clinical (unspecified phase)
0.8679	High Similarity	NPD6168	Clinical (unspecified phase)
0.8679	High Similarity	NPD6166	Phase 2
0.8671	High Similarity	NPD1240	Approved
0.8636	High Similarity	NPD1934	Approved
0.8581	High Similarity	NPD7819	Suspended
0.8581	High Similarity	NPD7421	Clinical (unspecified phase)
0.8552	High Similarity	NPD1607	Approved
0.8535	High Similarity	NPD4381	Clinical (unspecified phase)
0.8519	High Similarity	NPD7804	Clinical (unspecified phase)
0.8516	High Similarity	NPD6801	Discontinued
0.8418	Intermediate Similarity	NPD3749	Approved
0.8355	Intermediate Similarity	NPD6799	Approved
0.8276	Intermediate Similarity	NPD4907	Clinical (unspecified phase)
0.8242	Intermediate Similarity	NPD7074	Phase 3
0.8239	Intermediate Similarity	NPD4868	Clinical (unspecified phase)
0.8235	Intermediate Similarity	NPD1511	Approved
0.8228	Intermediate Similarity	NPD2801	Approved
0.8199	Intermediate Similarity	NPD5494	Approved
0.8182	Intermediate Similarity	NPD7054	Approved
0.8158	Intermediate Similarity	NPD3750	Approved
0.8153	Intermediate Similarity	NPD6599	Discontinued
0.8151	Intermediate Similarity	NPD6859	Clinical (unspecified phase)
0.8138	Intermediate Similarity	NPD4908	Phase 1
0.8133	Intermediate Similarity	NPD7472	Approved
0.8129	Intermediate Similarity	NPD1512	Approved
0.8125	Intermediate Similarity	NPD3882	Suspended
0.8117	Intermediate Similarity	NPD7390	Discontinued
0.8092	Intermediate Similarity	NPD2800	Approved
0.8084	Intermediate Similarity	NPD6797	Phase 2
0.8084	Intermediate Similarity	NPD7993	Clinical (unspecified phase)
0.8077	Intermediate Similarity	NPD5403	Approved
0.8072	Intermediate Similarity	NPD5844	Phase 1
0.8054	Intermediate Similarity	NPD6651	Approved
0.8036	Intermediate Similarity	NPD7251	Discontinued
0.8036	Intermediate Similarity	NPD6559	Discontinued
0.8013	Intermediate Similarity	NPD1551	Phase 2
0.7988	Intermediate Similarity	NPD6232	Discontinued
0.7988	Intermediate Similarity	NPD7808	Phase 3
0.7952	Intermediate Similarity	NPD7473	Discontinued
0.795	Intermediate Similarity	NPD3817	Phase 2
0.7949	Intermediate Similarity	NPD5401	Approved
0.7908	Intermediate Similarity	NPD970	Clinical (unspecified phase)
0.7904	Intermediate Similarity	NPD3818	Discontinued
0.7902	Intermediate Similarity	NPD1547	Clinical (unspecified phase)
0.7895	Intermediate Similarity	NPD2935	Discontinued
0.7882	Intermediate Similarity	NPD4419	Clinical (unspecified phase)
0.787	Intermediate Similarity	NPD5953	Discontinued
0.7857	Intermediate Similarity	NPD7286	Phase 2
0.7857	Intermediate Similarity	NPD1243	Approved
0.7848	Intermediate Similarity	NPD920	Approved
0.7843	Intermediate Similarity	NPD2344	Approved
0.7834	Intermediate Similarity	NPD2532	Approved
0.7834	Intermediate Similarity	NPD2534	Approved
0.7834	Intermediate Similarity	NPD2533	Approved
0.7829	Intermediate Similarity	NPD2799	Discontinued
0.7829	Intermediate Similarity	NPD3748	Approved
0.7821	Intermediate Similarity	NPD643	Clinical (unspecified phase)
0.7778	Intermediate Similarity	NPD4338	Clinical (unspecified phase)
0.7753	Intermediate Similarity	NPD8090	Clinical (unspecified phase)
0.7748	Intermediate Similarity	NPD5124	Phase 1
0.7748	Intermediate Similarity	NPD5123	Clinical (unspecified phase)
0.774	Intermediate Similarity	NPD4363	Phase 3
0.774	Intermediate Similarity	NPD4360	Phase 2
0.7733	Intermediate Similarity	NPD8312	Approved
0.7733	Intermediate Similarity	NPD8313	Approved
0.773	Intermediate Similarity	NPD5402	Approved
0.7722	Intermediate Similarity	NPD7004	Clinical (unspecified phase)
0.7722	Intermediate Similarity	NPD642	Clinical (unspecified phase)
0.7712	Intermediate Similarity	NPD1509	Clinical (unspecified phase)
0.7712	Intermediate Similarity	NPD7033	Discontinued
0.7692	Intermediate Similarity	NPD1878	Clinical (unspecified phase)
0.7692	Intermediate Similarity	NPD4628	Phase 3
0.7687	Intermediate Similarity	NPD1203	Approved
0.7669	Intermediate Similarity	NPD8455	Phase 2
0.7667	Intermediate Similarity	NPD2313	Discontinued
0.7662	Intermediate Similarity	NPD6100	Approved
0.7662	Intermediate Similarity	NPD6099	Approved
0.7655	Intermediate Similarity	NPD1610	Phase 2
0.7654	Intermediate Similarity	NPD7615	Clinical (unspecified phase)
0.7651	Intermediate Similarity	NPD6832	Phase 2
0.7643	Intermediate Similarity	NPD2309	Approved
0.764	Intermediate Similarity	NPD7458	Discontinued
0.764	Intermediate Similarity	NPD3226	Approved
0.764	Intermediate Similarity	NPD5808	Clinical (unspecified phase)
0.7627	Intermediate Similarity	NPD7879	Clinical (unspecified phase)
0.7622	Intermediate Similarity	NPD1548	Phase 1
0.758	Intermediate Similarity	NPD7003	Approved
0.755	Intermediate Similarity	NPD3268	Approved
0.755	Intermediate Similarity	NPD6798	Discontinued
0.7548	Intermediate Similarity	NPD5406	Approved
0.7548	Intermediate Similarity	NPD5405	Approved
0.7548	Intermediate Similarity	NPD5408	Approved
0.7548	Intermediate Similarity	NPD5404	Approved
0.7547	Intermediate Similarity	NPD7213	Phase 3
0.7547	Intermediate Similarity	NPD7212	Phase 2
0.7514	Intermediate Similarity	NPD8397	Clinical (unspecified phase)
0.75	Intermediate Similarity	NPD2346	Discontinued
0.7485	Intermediate Similarity	NPD919	Approved
0.7483	Intermediate Similarity	NPD9717	Approved
0.7468	Intermediate Similarity	NPD6398	Clinical (unspecified phase)
0.7456	Intermediate Similarity	NPD3787	Discontinued
0.7451	Intermediate Similarity	NPD943	Approved
0.745	Intermediate Similarity	NPD2797	Approved
0.7416	Intermediate Similarity	NPD4287	Approved
0.7415	Intermediate Similarity	NPD422	Phase 1
0.7412	Intermediate Similarity	NPD3926	Phase 2
0.7407	Intermediate Similarity	NPD6980	Clinical (unspecified phase)
0.7405	Intermediate Similarity	NPD2654	Approved
0.7403	Intermediate Similarity	NPD4362	Clinical (unspecified phase)
0.7403	Intermediate Similarity	NPD4361	Phase 2
0.74	Intermediate Similarity	NPD2798	Approved
0.7399	Intermediate Similarity	NPD1729	Discontinued
0.7396	Intermediate Similarity	NPD1247	Approved
0.7391	Intermediate Similarity	NPD7447	Phase 1
0.7384	Intermediate Similarity	NPD3751	Discontinued
0.7384	Intermediate Similarity	NPD7177	Discontinued
0.7383	Intermediate Similarity	NPD3225	Approved
0.7368	Intermediate Similarity	NPD4625	Phase 3
0.7353	Intermediate Similarity	NPD5711	Approved
0.7353	Intermediate Similarity	NPD7229	Phase 3
0.7353	Intermediate Similarity	NPD5710	Approved
0.7349	Intermediate Similarity	NPD1465	Phase 2
0.7338	Intermediate Similarity	NPD1612	Clinical (unspecified phase)
0.7338	Intermediate Similarity	NPD1613	Approved
0.7337	Intermediate Similarity	NPD6777	Approved
0.7337	Intermediate Similarity	NPD6782	Approved
0.7337	Intermediate Similarity	NPD6781	Approved
0.7337	Intermediate Similarity	NPD6778	Approved
0.7337	Intermediate Similarity	NPD6780	Approved
0.7337	Intermediate Similarity	NPD6776	Approved
0.7337	Intermediate Similarity	NPD6779	Approved
0.7333	Intermediate Similarity	NPD5889	Approved
0.7333	Intermediate Similarity	NPD5890	Approved
0.7302	Intermediate Similarity	NPD8151	Discontinued
0.729	Intermediate Similarity	NPD1933	Approved
0.7289	Intermediate Similarity	NPD7577	Discontinued
0.7287	Intermediate Similarity	NPD7584	Approved
0.7273	Intermediate Similarity	NPD7871	Phase 2
0.7273	Intermediate Similarity	NPD6233	Phase 2
0.7273	Intermediate Similarity	NPD7870	Phase 2
0.7261	Intermediate Similarity	NPD4308	Phase 3
0.726	Intermediate Similarity	NPD9545	Approved
0.7248	Intermediate Similarity	NPD3972	Approved
0.7243	Intermediate Similarity	NPD7501	Clinical (unspecified phase)
0.7239	Intermediate Similarity	NPD6273	Approved
0.7222	Intermediate Similarity	NPD6143	Clinical (unspecified phase)
0.7219	Intermediate Similarity	NPD3266	Approved
0.7219	Intermediate Similarity	NPD7696	Phase 3
0.7219	Intermediate Similarity	NPD7435	Discontinued
0.7219	Intermediate Similarity	NPD3267	Approved
0.7219	Intermediate Similarity	NPD7697	Approved
0.7219	Intermediate Similarity	NPD7698	Approved
0.7216	Intermediate Similarity	NPD6104	Discontinued
0.7208	Intermediate Similarity	NPD3764	Approved
0.7202	Intermediate Similarity	NPD4288	Approved
0.7197	Intermediate Similarity	NPD7097	Phase 1
0.7193	Intermediate Similarity	NPD7199	Phase 2
0.719	Intermediate Similarity	NPD1529	Clinical (unspecified phase)
0.7186	Intermediate Similarity	NPD6844	Discontinued
0.7184	Intermediate Similarity	NPD7893	Clinical (unspecified phase)
0.7181	Intermediate Similarity	NPD1201	Approved
0.7179	Intermediate Similarity	NPD1899	Clinical (unspecified phase)
0.7178	Intermediate Similarity	NPD7422	Clinical (unspecified phase)
0.717	Intermediate Similarity	NPD2343	Clinical (unspecified phase)
0.7169	Intermediate Similarity	NPD6585	Discontinued
0.7168	Intermediate Similarity	NPD7784	Clinical (unspecified phase)
0.7153	Intermediate Similarity	NPD1241	Discontinued
0.7135	Intermediate Similarity	NPD7782	Clinical (unspecified phase)
0.7135	Intermediate Similarity	NPD7783	Phase 2
0.7133	Intermediate Similarity	NPD1608	Approved
0.7125	Intermediate Similarity	NPD2424	Discontinued
0.7124	Intermediate Similarity	NPD2861	Phase 2
0.7124	Intermediate Similarity	NPD1530	Clinical (unspecified phase)
0.7123	Intermediate Similarity	NPD9493	Approved
0.7111	Intermediate Similarity	NPD8150	Discontinued
0.711	Intermediate Similarity	NPD7184	Clinical (unspecified phase)
0.7108	Intermediate Similarity	NPD8158	Clinical (unspecified phase)
0.7105	Intermediate Similarity	NPD1470	Approved
0.7101	Intermediate Similarity	NPD2296	Approved
0.7097	Intermediate Similarity	NPD6410	Clinical (unspecified phase)
0.7097	Intermediate Similarity	NPD1296	Phase 2
0.7086	Intermediate Similarity	NPD4749	Approved
0.7081	Intermediate Similarity	NPD1652	Phase 2

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