NPASS Compound

Structure

NPC469420 OpenBabel07101719132D 68 77 0 0 1 0 0 0 0 0999 V2000 0.2392 -2.0126 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.6353 -5.9572 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0131 -1.1908 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2150 3.7541 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.1114 1.4632 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2446 3.9332 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5451 2.8241 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.2003 1.0840 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.8952 0.8638 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6042 3.1824 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9047 2.0733 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0731 0.1055 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7681 -0.1148 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.9868 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.8683 -3.3435 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1253 -1.1121 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7069 -4.4573 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -11.0367 -3.0953 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9275 -4.1260 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3169 0.9300 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.6916 -2.8303 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9343 2.2524 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.8570 -0.4940 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -7.1288 -2.6901 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.3304 -0.5259 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.8433 -3.4345 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -10.7728 -4.0461 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.0222 -3.7332 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -11.4644 -4.7501 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.2294 -4.3208 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -11.2005 -5.7010 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.3242 -3.9280 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -10.2451 -5.9479 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.2117 -2.9476 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.2939 1.5016 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.7298 -1.4726 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.5536 -5.2440 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.0045 -2.3600 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.4257 -0.5570 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.6256 -3.9312 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.4609 -1.3172 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.8222 -4.9883 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.9868 0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.4755 -3.4297 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.9868 -0.9868 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -7.2150 -4.0830 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -11.9921 -2.8483 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.3110 -0.4154 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.7812 -3.1276 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -12.4198 -4.5031 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.3419 -5.3011 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -11.8921 -6.4049 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.5314 -4.5155 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -9.9813 -6.8988 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.3065 -2.5548 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.6240 0.5717 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.5137 -2.0720 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.4024 -0.4157 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.7203 -3.5384 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.6765 1.6808 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.8188 -1.8517 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -9.8174 -4.2931 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.9098 -2.7528 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.5982 -5.4909 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.8921 -1.3796 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.1628 -1.2156 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.8399 -4.8945 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 42 1 0 0 0 0 2 43 1 0 0 0 0 3 59 1 0 0 0 0 4 6 2 0 0 0 0 4 7 1 0 0 0 0 5 8 2 0 0 0 0 5 9 1 0 0 0 0 6 10 1 0 0 0 0 7 11 2 0 0 0 0 8 12 1 0 0 0 0 9 13 2 0 0 0 0 10 22 2 0 0 0 0 11 22 1 0 0 0 0 12 23 2 0 0 0 0 13 23 1 0 0 0 0 14 24 1 0 0 0 0 14 46 1 0 0 0 0 15 25 1 0 0 0 0 15 47 1 0 0 0 0 16 26 1 0 0 0 0 16 42 1 0 0 0 0 17 27 1 0 0 0 0 17 43 1 0 0 0 0 18 48 1 0 0 0 0 19 60 1 0 0 0 0 20 44 1 0 0 0 0 20 61 1 0 0 0 0 21 45 1 0 0 0 0 21 62 1 0 0 0 0 22 36 1 0 0 0 0 23 37 1 0 0 0 0 24 26 1 0 0 0 0 24 44 1 1 0 0 0 25 27 1 0 0 0 0 25 45 1 1 0 0 0 26 49 2 0 0 0 0 27 50 2 0 0 0 0 28 18 1 1 0 0 0 28 30 1 0 0 0 0 28 63 1 0 0 0 0 29 19 1 1 0 0 0 29 31 1 0 0 0 0 29 64 1 0 0 0 0 30 32 1 0 0 0 0 30 51 1 6 0 0 0 31 33 1 0 0 0 0 31 52 1 6 0 0 0 32 34 1 0 0 0 0 32 53 1 1 0 0 0 33 35 1 0 0 0 0 33 54 1 1 0 0 0 34 38 1 0 0 0 0 34 55 1 6 0 0 0 35 39 1 0 0 0 0 35 56 1 6 0 0 0 36 57 2 0 0 0 0 36 61 1 0 0 0 0 37 58 2 0 0 0 0 37 62 1 0 0 0 0 38 63 1 0 0 0 0 38 65 1 1 0 0 0 39 64 1 0 0 0 0 39 66 1 1 0 0 0 40 44 1 6 0 0 0 40 59 1 0 0 0 0 40 67 1 0 0 0 0 41 45 1 1 0 0 0 41 60 1 0 0 0 0 41 68 1 0 0 0 0 42 46 1 1 0 0 0 42 67 1 0 0 0 0 43 47 1 6 0 0 0 43 68 1 0 0 0 0 44 46 1 1 0 0 0 45 47 1 6 0 0 0 46 66 1 6 0 0 0 47 65 1 1 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	956.33
Volume:	894.133
LogP:	1.441
LogD:	0.711
LogS:	-3.732
# Rotatable Bonds:	17
TPSA:	302.19
# H-Bond Aceptor:	21
# H-Bond Donor:	7
# Rings:	12
# Heavy Atoms:	21

MedChem Properties

QED Drug-Likeness Score:	0.102
Synthetic Accessibility Score:	7.872
Fsp3:	0.66
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.654
MDCK Permeability:	7.686950993956998e-05
Pgp-inhibitor:	0.41
Pgp-substrate:	1.0
Human Intestinal Absorption (HIA):	0.812
20% Bioavailability (F20%):	0.653
30% Bioavailability (F30%):	0.996

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.15
Plasma Protein Binding (PPB):	44.79497146606445%
Volume Distribution (VD):	0.322
Pgp-substrate:	15.452682495117188%

ADMET: Metabolism

CYP1A2-inhibitor:	0.001
CYP1A2-substrate:	0.998
CYP2C19-inhibitor:	0.007
CYP2C19-substrate:	0.27
CYP2C9-inhibitor:	0.003
CYP2C9-substrate:	0.001
CYP2D6-inhibitor:	0.002
CYP2D6-substrate:	0.03
CYP3A4-inhibitor:	0.304
CYP3A4-substrate:	0.256

ADMET: Excretion

Clearance (CL):	1.355
Half-life (T1/2):	0.64

ADMET: Toxicity

hERG Blockers:	0.125
Human Hepatotoxicity (H-HT):	0.143
Drug-inuced Liver Injury (DILI):	0.909
AMES Toxicity:	0.964
Rat Oral Acute Toxicity:	0.84
Maximum Recommended Daily Dose:	0.015
Skin Sensitization:	0.795
Carcinogencity:	0.865
Eye Corrosion:	0.003
Eye Irritation:	0.013
Respiratory Toxicity:	0.924

Download Data

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

Natural Product: NPC469420

Natural Product ID:	NPC469420
*Common Name:**	Paeonidanin D
IUPAC Name:	n.a.
Synonyms:	Paeonidanin D
Standard InCHIKey:	QDMFASNVGVOIEZ-ASJHKIPBSA-N
Standard InCHI:	InChI=1S/C47H56O21/c1-42-16-26(49)24-14-46(42,44(24,40(59-3)67-42)20-61-36(57)22-10-6-4-7-11-22)66-39-35(56)33(54)31(52)29(64-39)19-60-41-45(21-62-37(58)23-12-8-5-9-13-23)25-15-47(45,43(2,68-41)17-27(25)50)65-38-34(55)32(53)30(51)28(18-48)63-38/h4-13,24-25,28-35,38-41,48,51-56H,14-21H2,1-3H3/t24-,25-,28-,29-,30-,31-,32+,33+,34-,35-,38+,39+,40+,41+,42+,43+,44+,45+,46-,47-/m1/s1
SMILES:	OC[C@H]1O[C@@H](O[C@]23C[C@H]4[C@@]3(COC(=O)c3ccccc3)[C@H](O[C@@]2(C)CC4=O)OC[C@H]2O[C@@H](O[C@]34C[C@H]5[C@@]4(COC(=O)c4ccccc4)[C@H](O[C@@]3(C)CC5=O)OC)[C@@H]([C@H]([C@@H]2O)O)O)[C@@H]([C@H]([C@@H]1O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL1078415
PubChem CID:	46883514
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0002049] Terpene glycosides

*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
NPO30226	Paeonia albiflora	Species	Paeoniaceae	Eukaryota	roots	n.a.	n.a.	PMID[19691309]
NPO30226	Paeonia albiflora	Species	Paeoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO30226	Paeonia albiflora	Species	Paeoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]

☑ 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	4

Activity Type	# Activity
Cell Line	4

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT848	Cell Line	N9	Homo sapiens	Inhibition	=	111.5	%	PMID[461267]
NPT848	Cell Line	N9	Homo sapiens	Inhibition	=	96.6	%	PMID[461267]
NPT848	Cell Line	N9	Homo sapiens	Inhibition	=	83.5	%	PMID[461267]
NPT848	Cell Line	N9	Homo sapiens	Inhibition	=	77.1	%	PMID[461267]

☑ 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 NPC469420 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	406
0.1-0.2	1442
0.2-0.3	2941
0.3-0.4	6408
0.4-0.5	11226
0.5-0.6	12903
0.6-0.7	6224
0.7-0.8	996
0.8-0.85	102
0.85-0.9	31
0.9-0.95	16
0.95-1	2

Similarity Score	Similarity Level	Natural Product ID
0.9748	High Similarity	NPC469421
0.9419	High Similarity	NPC469417
0.9236	High Similarity	NPC469399
0.9177	High Similarity	NPC477623
0.9125	High Similarity	NPC150893
0.9125	High Similarity	NPC329960
0.9125	High Similarity	NPC295408
0.908	High Similarity	NPC477471
0.908	High Similarity	NPC477473
0.908	High Similarity	NPC477466
0.908	High Similarity	NPC477469
0.9045	High Similarity	NPC34066
0.9045	High Similarity	NPC469422
0.9038	High Similarity	NPC477905
0.9032	High Similarity	NPC469448
0.9018	High Similarity	NPC102465
0.8981	High Similarity	NPC469477
0.8981	High Similarity	NPC133430
0.8924	High Similarity	NPC5115
0.8924	High Similarity	NPC469398
0.8917	High Similarity	NPC472548
0.8862	High Similarity	NPC477617
0.8854	High Similarity	NPC469415
0.8848	High Similarity	NPC469419
0.8839	High Similarity	NPC469513
0.8812	High Similarity	NPC477735
0.8805	High Similarity	NPC472549
0.879	High Similarity	NPC222102
0.879	High Similarity	NPC303429
0.878	High Similarity	NPC477491
0.8758	High Similarity	NPC477736
0.875	High Similarity	NPC106895
0.8742	High Similarity	NPC472030
0.8742	High Similarity	NPC242262
0.8742	High Similarity	NPC472022
0.8742	High Similarity	NPC237549
0.8742	High Similarity	NPC257213
0.8742	High Similarity	NPC265395
0.8742	High Similarity	NPC249471
0.8742	High Similarity	NPC473414
0.8742	High Similarity	NPC1173
0.8742	High Similarity	NPC472005
0.8742	High Similarity	NPC256142
0.8742	High Similarity	NPC304876
0.8742	High Similarity	NPC158333
0.8735	High Similarity	NPC477488
0.8688	High Similarity	NPC228204
0.8688	High Similarity	NPC114410
0.8688	High Similarity	NPC26033
0.8688	High Similarity	NPC282239
0.8688	High Similarity	NPC112523
0.8671	High Similarity	NPC7095
0.8659	High Similarity	NPC66193
0.8642	High Similarity	NPC471102
0.8634	High Similarity	NPC217091
0.8625	High Similarity	NPC472658
0.8625	High Similarity	NPC472657
0.8625	High Similarity	NPC69425
0.8625	High Similarity	NPC77719
0.8623	High Similarity	NPC149002
0.8623	High Similarity	NPC469396
0.8623	High Similarity	NPC469459
0.8623	High Similarity	NPC469458
0.8623	High Similarity	NPC88176
0.8608	High Similarity	NPC250046
0.8608	High Similarity	NPC81698
0.8608	High Similarity	NPC60509
0.8606	High Similarity	NPC471493
0.8606	High Similarity	NPC471134
0.8606	High Similarity	NPC477627
0.858	High Similarity	NPC469771
0.858	High Similarity	NPC472393
0.8571	High Similarity	NPC469456
0.8554	High Similarity	NPC473468
0.8554	High Similarity	NPC61891
0.8554	High Similarity	NPC475567
0.8554	High Similarity	NPC473557
0.8553	High Similarity	NPC198455
0.8553	High Similarity	NPC112216
0.8553	High Similarity	NPC161239
0.8553	High Similarity	NPC165260
0.8535	High Similarity	NPC70403
0.8535	High Similarity	NPC470159
0.8535	High Similarity	NPC158663
0.8535	High Similarity	NPC472572
0.8535	High Similarity	NPC200471
0.8535	High Similarity	NPC476973
0.8535	High Similarity	NPC472568
0.8535	High Similarity	NPC177940
0.8535	High Similarity	NPC184817
0.8535	High Similarity	NPC174982
0.8535	High Similarity	NPC471104
0.8535	High Similarity	NPC29704
0.8535	High Similarity	NPC473088
0.8535	High Similarity	NPC171525
0.8535	High Similarity	NPC472575
0.8535	High Similarity	NPC469349
0.8535	High Similarity	NPC472571
0.8535	High Similarity	NPC470157
0.8535	High Similarity	NPC96903
0.8528	High Similarity	NPC476784
0.8528	High Similarity	NPC477467
0.8516	High Similarity	NPC77493
0.8503	High Similarity	NPC475531
0.8503	High Similarity	NPC475175
0.8503	High Similarity	NPC475198
0.85	High Similarity	NPC329657
0.85	High Similarity	NPC470153
0.85	High Similarity	NPC51602
0.85	High Similarity	NPC471103
0.8491	Intermediate Similarity	NPC471101
0.8491	Intermediate Similarity	NPC270590
0.8491	Intermediate Similarity	NPC92293
0.8491	Intermediate Similarity	NPC301556
0.8491	Intermediate Similarity	NPC266265
0.8471	Intermediate Similarity	NPC475122
0.8471	Intermediate Similarity	NPC472569
0.8471	Intermediate Similarity	NPC188865
0.8471	Intermediate Similarity	NPC125106
0.8471	Intermediate Similarity	NPC11685
0.8471	Intermediate Similarity	NPC25768
0.8471	Intermediate Similarity	NPC472573
0.8471	Intermediate Similarity	NPC70716
0.8471	Intermediate Similarity	NPC470152
0.8471	Intermediate Similarity	NPC163719
0.8471	Intermediate Similarity	NPC95265
0.8471	Intermediate Similarity	NPC472570
0.8471	Intermediate Similarity	NPC241951
0.8471	Intermediate Similarity	NPC95810
0.8471	Intermediate Similarity	NPC57628
0.8471	Intermediate Similarity	NPC475759
0.8471	Intermediate Similarity	NPC476974
0.8466	Intermediate Similarity	NPC477470
0.8466	Intermediate Similarity	NPC477474
0.8466	Intermediate Similarity	NPC477472
0.8457	Intermediate Similarity	NPC473670
0.8457	Intermediate Similarity	NPC21410
0.8452	Intermediate Similarity	NPC40138
0.8439	Intermediate Similarity	NPC469418
0.8438	Intermediate Similarity	NPC470245
0.8438	Intermediate Similarity	NPC473214
0.8438	Intermediate Similarity	NPC254558
0.8428	Intermediate Similarity	NPC281717
0.8421	Intermediate Similarity	NPC148185
0.8418	Intermediate Similarity	NPC472556
0.8418	Intermediate Similarity	NPC127857
0.8408	Intermediate Similarity	NPC163087
0.8391	Intermediate Similarity	NPC195114
0.8383	Intermediate Similarity	NPC293568
0.8383	Intermediate Similarity	NPC117943
0.8375	Intermediate Similarity	NPC476975
0.8375	Intermediate Similarity	NPC473215
0.8373	Intermediate Similarity	NPC477188
0.8373	Intermediate Similarity	NPC43304
0.8373	Intermediate Similarity	NPC55744
0.8373	Intermediate Similarity	NPC477190
0.8373	Intermediate Similarity	NPC275477
0.8365	Intermediate Similarity	NPC477737
0.8344	Intermediate Similarity	NPC475513
0.8344	Intermediate Similarity	NPC473755
0.8333	Intermediate Similarity	NPC260300
0.8333	Intermediate Similarity	NPC80360
0.8323	Intermediate Similarity	NPC478073
0.8323	Intermediate Similarity	NPC91730
0.8314	Intermediate Similarity	NPC13989
0.8313	Intermediate Similarity	NPC476077
0.8291	Intermediate Similarity	NPC91703
0.8284	Intermediate Similarity	NPC120012
0.828	Intermediate Similarity	NPC291599
0.828	Intermediate Similarity	NPC16912
0.828	Intermediate Similarity	NPC118080
0.828	Intermediate Similarity	NPC97947
0.828	Intermediate Similarity	NPC41481
0.828	Intermediate Similarity	NPC472576
0.828	Intermediate Similarity	NPC27377
0.828	Intermediate Similarity	NPC87448
0.8272	Intermediate Similarity	NPC101043
0.8272	Intermediate Similarity	NPC197037
0.8272	Intermediate Similarity	NPC306799
0.825	Intermediate Similarity	NPC474935
0.8242	Intermediate Similarity	NPC318447
0.8242	Intermediate Similarity	NPC322048
0.8239	Intermediate Similarity	NPC111466
0.8239	Intermediate Similarity	NPC188217
0.8235	Intermediate Similarity	NPC265600
0.8232	Intermediate Similarity	NPC473611
0.8232	Intermediate Similarity	NPC469730
0.8232	Intermediate Similarity	NPC132599
0.8232	Intermediate Similarity	NPC473632
0.8217	Intermediate Similarity	NPC473060
0.8217	Intermediate Similarity	NPC473085
0.8217	Intermediate Similarity	NPC4341
0.8217	Intermediate Similarity	NPC275592
0.8217	Intermediate Similarity	NPC473112
0.8217	Intermediate Similarity	NPC200592
0.8217	Intermediate Similarity	NPC147880
0.8217	Intermediate Similarity	NPC97667
0.8217	Intermediate Similarity	NPC473109
0.8217	Intermediate Similarity	NPC477904
0.8217	Intermediate Similarity	NPC43241

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 NPC469420 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	339
0.1-0.2	813
0.2-0.3	1996
0.3-0.4	3245
0.4-0.5	1984
0.5-0.6	618
0.6-0.7	140
0.7-0.8	15
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8246	Intermediate Similarity	NPD7799	Discontinued
0.7921	Intermediate Similarity	NPD8407	Phase 2
0.7853	Intermediate Similarity	NPD8368	Discontinued
0.7765	Intermediate Similarity	NPD8312	Approved
0.7765	Intermediate Similarity	NPD8313	Approved
0.7684	Intermediate Similarity	NPD8470	Clinical (unspecified phase)
0.7663	Intermediate Similarity	NPD7879	Clinical (unspecified phase)
0.765	Intermediate Similarity	NPD8435	Approved
0.765	Intermediate Similarity	NPD8360	Approved
0.765	Intermediate Similarity	NPD8361	Approved
0.7637	Intermediate Similarity	NPD8434	Phase 2
0.7566	Intermediate Similarity	NPD8486	Clinical (unspecified phase)
0.7541	Intermediate Similarity	NPD8424	Clinical (unspecified phase)
0.753	Intermediate Similarity	NPD7236	Approved
0.75	Intermediate Similarity	NPD7966	Clinical (unspecified phase)
0.7486	Intermediate Similarity	NPD8055	Clinical (unspecified phase)
0.743	Intermediate Similarity	NPD7228	Approved
0.7421	Intermediate Similarity	NPD5952	Clinical (unspecified phase)
0.7412	Intermediate Similarity	NPD7239	Suspended
0.7409	Intermediate Similarity	NPD8320	Phase 1
0.7409	Intermediate Similarity	NPD8319	Approved
0.7407	Intermediate Similarity	NPD8485	Approved
0.7368	Intermediate Similarity	NPD7699	Phase 2
0.7368	Intermediate Similarity	NPD7700	Phase 2
0.7363	Intermediate Similarity	NPD7240	Approved
0.7351	Intermediate Similarity	NPD8150	Discontinued
0.7299	Intermediate Similarity	NPD8455	Phase 2
0.7267	Intermediate Similarity	NPD7458	Discontinued
0.7211	Intermediate Similarity	NPD6535	Approved
0.7211	Intermediate Similarity	NPD6534	Approved
0.7198	Intermediate Similarity	NPD7804	Clinical (unspecified phase)
0.7181	Intermediate Similarity	NPD8397	Clinical (unspecified phase)
0.7179	Intermediate Similarity	NPD7435	Discontinued
0.7174	Intermediate Similarity	NPD7685	Pre-registration
0.7172	Intermediate Similarity	NPD8151	Discontinued
0.7158	Intermediate Similarity	NPD7074	Phase 3
0.7158	Intermediate Similarity	NPD7472	Approved
0.7135	Intermediate Similarity	NPD7808	Phase 3
0.7135	Intermediate Similarity	NPD8389	Clinical (unspecified phase)
0.7119	Intermediate Similarity	NPD4965	Approved
0.7119	Intermediate Similarity	NPD4967	Phase 2
0.7119	Intermediate Similarity	NPD4966	Approved
0.7104	Intermediate Similarity	NPD7054	Approved
0.7092	Intermediate Similarity	NPD7698	Approved
0.7092	Intermediate Similarity	NPD7697	Approved
0.7092	Intermediate Similarity	NPD7696	Phase 3
0.7081	Intermediate Similarity	NPD7251	Discontinued
0.7079	Intermediate Similarity	NPD4381	Clinical (unspecified phase)
0.705	Intermediate Similarity	NPD7874	Approved
0.705	Intermediate Similarity	NPD7875	Clinical (unspecified phase)
0.7049	Intermediate Similarity	NPD3818	Discontinued
0.7039	Intermediate Similarity	NPD6234	Discontinued
0.7035	Intermediate Similarity	NPD7701	Phase 2
0.7027	Intermediate Similarity	NPD6797	Phase 2
0.7026	Intermediate Similarity	NPD6782	Approved
0.7026	Intermediate Similarity	NPD6780	Approved
0.7026	Intermediate Similarity	NPD6781	Approved
0.7026	Intermediate Similarity	NPD6779	Approved
0.7026	Intermediate Similarity	NPD6778	Approved
0.7026	Intermediate Similarity	NPD6776	Approved
0.7026	Intermediate Similarity	NPD6777	Approved
0.7022	Intermediate Similarity	NPD7058	Phase 2
0.7022	Intermediate Similarity	NPD7057	Phase 3
0.6989	Remote Similarity	NPD6559	Discontinued
0.698	Remote Similarity	NPD8462	Phase 1
0.6979	Remote Similarity	NPD6213	Phase 3
0.6979	Remote Similarity	NPD6214	Clinical (unspecified phase)
0.6979	Remote Similarity	NPD6212	Phase 3
0.697	Remote Similarity	NPD7870	Phase 2
0.697	Remote Similarity	NPD7871	Phase 2
0.6949	Remote Similarity	NPD37	Approved
0.6935	Remote Similarity	NPD7993	Clinical (unspecified phase)
0.6931	Remote Similarity	NPD7801	Approved
0.6923	Remote Similarity	NPD7266	Discontinued
0.691	Remote Similarity	NPD7819	Suspended
0.6901	Remote Similarity	NPD8166	Discontinued
0.6901	Remote Similarity	NPD4628	Phase 3
0.6899	Remote Similarity	NPD5125	Phase 3
0.6899	Remote Similarity	NPD5126	Approved
0.6869	Remote Similarity	NPD6823	Phase 2
0.6868	Remote Similarity	NPD8127	Discontinued
0.6862	Remote Similarity	NPD4338	Clinical (unspecified phase)
0.6855	Remote Similarity	NPD8328	Phase 3
0.6847	Remote Similarity	NPD7782	Clinical (unspecified phase)
0.6847	Remote Similarity	NPD7783	Phase 2
0.6845	Remote Similarity	NPD8404	Phase 2
0.6836	Remote Similarity	NPD4380	Phase 2
0.6831	Remote Similarity	NPD3787	Discontinued
0.6816	Remote Similarity	NPD5760	Phase 2
0.6816	Remote Similarity	NPD5761	Phase 2
0.6816	Remote Similarity	NPD7096	Clinical (unspecified phase)
0.6813	Remote Similarity	NPD5494	Approved
0.6811	Remote Similarity	NPD7473	Discontinued
0.6807	Remote Similarity	NPD7961	Discontinued
0.6796	Remote Similarity	NPD7075	Discontinued
0.6788	Remote Similarity	NPD7008	Discontinued
0.6782	Remote Similarity	NPD6143	Clinical (unspecified phase)
0.6776	Remote Similarity	NPD7199	Phase 2
0.6774	Remote Similarity	NPD3751	Discontinued
0.6761	Remote Similarity	NPD6980	Clinical (unspecified phase)
0.6757	Remote Similarity	NPD6166	Phase 2
0.6757	Remote Similarity	NPD6167	Clinical (unspecified phase)
0.6757	Remote Similarity	NPD6168	Clinical (unspecified phase)
0.675	Remote Similarity	NPD7680	Approved
0.674	Remote Similarity	NPD4868	Clinical (unspecified phase)
0.6738	Remote Similarity	NPD5844	Phase 1
0.673	Remote Similarity	NPD8516	Approved
0.673	Remote Similarity	NPD8513	Phase 3
0.673	Remote Similarity	NPD8515	Approved
0.673	Remote Similarity	NPD8517	Approved
0.6717	Remote Similarity	NPD7237	Clinical (unspecified phase)
0.6714	Remote Similarity	NPD8155	Clinical (unspecified phase)
0.6707	Remote Similarity	NPD6007	Clinical (unspecified phase)
0.6705	Remote Similarity	NPD6273	Approved
0.6685	Remote Similarity	NPD6591	Clinical (unspecified phase)
0.6685	Remote Similarity	NPD8443	Clinical (unspecified phase)
0.6685	Remote Similarity	NPD6959	Discontinued
0.6683	Remote Similarity	NPD7211	Clinical (unspecified phase)
0.6667	Remote Similarity	NPD7497	Discontinued
0.6667	Remote Similarity	NPD7852	Clinical (unspecified phase)
0.6667	Remote Similarity	NPD5537	Clinical (unspecified phase)
0.6667	Remote Similarity	NPD6190	Approved
0.6649	Remote Similarity	NPD6232	Discontinued
0.6648	Remote Similarity	NPD6599	Discontinued
0.6648	Remote Similarity	NPD7004	Clinical (unspecified phase)
0.6647	Remote Similarity	NPD3764	Approved
0.6646	Remote Similarity	NPD7319	Approved
0.6628	Remote Similarity	NPD7702	Clinical (unspecified phase)
0.6613	Remote Similarity	NPD7184	Clinical (unspecified phase)
0.6611	Remote Similarity	NPD7411	Suspended
0.6601	Remote Similarity	NPD7999	Approved
0.6592	Remote Similarity	NPD3226	Approved
0.6587	Remote Similarity	NPD7930	Approved
0.6575	Remote Similarity	NPD6801	Discontinued
0.6564	Remote Similarity	NPD7507	Approved
0.655	Remote Similarity	NPD7097	Phase 1
0.6545	Remote Similarity	NPD6764	Approved
0.6545	Remote Similarity	NPD6765	Approved
0.6538	Remote Similarity	NPD2393	Clinical (unspecified phase)
0.6532	Remote Similarity	NPD2346	Discontinued
0.6522	Remote Similarity	NPD3749	Approved
0.6519	Remote Similarity	NPD2629	Approved
0.6514	Remote Similarity	NPD7003	Approved
0.6503	Remote Similarity	NPD5402	Approved
0.6503	Remote Similarity	NPD3817	Phase 2
0.6495	Remote Similarity	NPD5619	Clinical (unspecified phase)
0.6485	Remote Similarity	NPD7736	Approved
0.6484	Remote Similarity	NPD1934	Approved
0.6481	Remote Similarity	NPD3412	Clinical (unspecified phase)
0.6481	Remote Similarity	NPD8058	Clinical (unspecified phase)
0.6481	Remote Similarity	NPD8059	Phase 3
0.6478	Remote Similarity	NPD8295	Clinical (unspecified phase)
0.6478	Remote Similarity	NPD4198	Discontinued
0.6474	Remote Similarity	NPD2181	Clinical (unspecified phase)
0.6467	Remote Similarity	NPD7768	Phase 2
0.6464	Remote Similarity	NPD7028	Phase 2
0.6461	Remote Similarity	NPD2533	Approved
0.6461	Remote Similarity	NPD7422	Clinical (unspecified phase)
0.6461	Remote Similarity	NPD2532	Approved
0.6461	Remote Similarity	NPD2534	Approved
0.646	Remote Similarity	NPD7741	Discontinued
0.6457	Remote Similarity	NPD7421	Clinical (unspecified phase)
0.6442	Remote Similarity	NPD7457	Clinical (unspecified phase)
0.642	Remote Similarity	NPD8033	Approved
0.6415	Remote Similarity	NPD5951	Approved
0.641	Remote Similarity	NPD6785	Approved
0.641	Remote Similarity	NPD6784	Approved
0.6409	Remote Similarity	NPD5808	Clinical (unspecified phase)
0.6404	Remote Similarity	NPD6799	Approved
0.6389	Remote Similarity	NPD5403	Approved
0.6386	Remote Similarity	NPD8285	Discontinued
0.6379	Remote Similarity	NPD5406	Approved
0.6379	Remote Similarity	NPD5404	Approved
0.6379	Remote Similarity	NPD5405	Approved
0.6379	Remote Similarity	NPD5408	Approved
0.6378	Remote Similarity	NPD3882	Suspended
0.6369	Remote Similarity	NPD7410	Clinical (unspecified phase)
0.6369	Remote Similarity	NPD5401	Approved
0.6364	Remote Similarity	NPD6674	Discontinued
0.6359	Remote Similarity	NPD1465	Phase 2
0.6358	Remote Similarity	NPD8377	Approved
0.6358	Remote Similarity	NPD8294	Approved
0.6322	Remote Similarity	NPD2799	Discontinued
0.6319	Remote Similarity	NPD8380	Approved
0.6319	Remote Similarity	NPD8378	Approved
0.6319	Remote Similarity	NPD8379	Approved
0.6319	Remote Similarity	NPD8296	Approved
0.6319	Remote Similarity	NPD8335	Approved
0.6313	Remote Similarity	NPD7390	Discontinued
0.6296	Remote Similarity	NPD7610	Discontinued
0.6289	Remote Similarity	NPD8133	Approved
0.6282	Remote Similarity	NPD6686	Approved
0.628	Remote Similarity	NPD7163	Clinical (unspecified phase)
0.6276	Remote Similarity	NPD7090	Clinical (unspecified phase)
0.627	Remote Similarity	NPD2801	Approved
0.6257	Remote Similarity	NPD2313	Discontinued
0.625	Remote Similarity	NPD2343	Clinical (unspecified phase)
0.625	Remote Similarity	NPD6010	Discontinued
0.625	Remote Similarity	NPD7584	Approved
0.6243	Remote Similarity	NPD230	Phase 1

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