NPASS Compound

Structure

CID84684 OpenBabel06191715422D 50 56 0 0 1 0 0 0 0 0999 V2000 1.4732 -1.9651 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3331 2.9360 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2462 -7.1322 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.0660 -1.7135 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7372 1.9951 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5111 -0.3861 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8323 -5.6375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.3655 0.3886 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1370 -1.3740 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3331 0.0885 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5390 -6.5402 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.1334 0.9465 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0809 -1.2748 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0113 -3.1623 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3974 -2.2952 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6891 1.0377 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2688 -5.1295 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.3319 -0.9414 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9651 0.2609 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1045 -1.6266 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7679 -1.3300 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6891 0.0885 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1972 -4.9321 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.4648 -0.5554 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5791 -0.6061 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9326 -3.2615 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4905 -2.4937 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3331 1.0377 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6106 -6.7375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.0005 0.5604 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4670 -0.4077 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5111 1.5122 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0245 -6.0322 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.0997 -0.3835 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9091 0.3602 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8671 -0.3861 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.4905 -4.0294 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.3932 -2.7870 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.6351 -0.7054 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.1605 -1.5273 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.1551 1.5122 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.3173 -7.6402 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.7684 1.1183 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.4109 -0.3085 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5111 2.4614 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.9529 -6.2295 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.9668 -0.7696 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.2951 1.2273 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.3932 -3.7361 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 21 2 0 0 0 0 2 45 1 0 0 0 0 3 46 1 0 0 0 0 4 47 1 0 0 0 0 5 48 1 0 0 0 0 6 10 2 0 0 0 0 6 22 1 0 0 0 0 7 11 2 0 0 0 0 7 23 1 0 0 0 0 8 12 2 0 0 0 0 8 24 1 0 0 0 0 9 13 2 0 0 0 0 9 25 1 0 0 0 0 10 28 1 0 0 0 0 11 29 1 0 0 0 0 12 30 1 0 0 0 0 13 31 1 0 0 0 0 14 15 1 0 0 0 0 14 26 1 0 0 0 0 16 22 2 0 0 0 0 16 32 1 0 0 0 0 17 23 2 0 0 0 0 17 33 1 0 0 0 0 18 24 2 0 0 0 0 18 34 1 0 0 0 0 19 25 2 0 0 0 0 19 35 1 0 0 0 0 20 27 1 0 0 0 0 20 40 1 0 0 0 0 21 36 1 0 0 0 0 21 40 1 0 0 0 0 25 39 1 0 0 0 0 26 27 2 0 0 0 0 26 37 1 0 0 0 0 27 38 1 0 0 0 0 28 32 2 0 0 0 0 28 41 1 0 0 0 0 29 33 2 0 0 0 0 29 42 1 0 0 0 0 30 34 2 0 0 0 0 30 43 1 0 0 0 0 31 35 2 0 0 0 0 31 44 1 0 0 0 0 32 45 1 0 0 0 0 33 46 1 0 0 0 0 34 47 1 0 0 0 0 35 48 1 0 0 0 0 36 22 1 1 0 0 0 36 50 1 0 0 0 0 37 23 1 6 0 0 0 37 49 1 0 0 0 0 38 24 1 6 0 0 0 38 49 1 0 0 0 0 39 40 1 1 0 0 0 39 50 1 0 0 0 0 40 15 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	680.26
Volume:	691.492
LogP:	4.932
LogD:	3.339
LogS:	-4.47
# Rotatable Bonds:	8
TPSA:	136.3
# H-Bond Aceptor:	10
# H-Bond Donor:	4
# Rings:	7
# Heavy Atoms:	10

MedChem Properties

QED Drug-Likeness Score:	0.136
Synthetic Accessibility Score:	5.181
Fsp3:	0.3
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	1
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.641
MDCK Permeability:	6.091339400882134e-06
Pgp-inhibitor:	0.324
Pgp-substrate:	0.968
Human Intestinal Absorption (HIA):	0.012
20% Bioavailability (F20%):	0.142
30% Bioavailability (F30%):	0.787

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.002
Plasma Protein Binding (PPB):	95.088134765625%
Volume Distribution (VD):	0.361
Pgp-substrate:	6.453862190246582%

ADMET: Metabolism

CYP1A2-inhibitor:	0.019
CYP1A2-substrate:	0.867
CYP2C19-inhibitor:	0.592
CYP2C19-substrate:	0.22
CYP2C9-inhibitor:	0.714
CYP2C9-substrate:	0.918
CYP2D6-inhibitor:	0.028
CYP2D6-substrate:	0.932
CYP3A4-inhibitor:	0.523
CYP3A4-substrate:	0.874

ADMET: Excretion

Clearance (CL):	7.19
Half-life (T1/2):	0.234

ADMET: Toxicity

hERG Blockers:	0.124
Human Hepatotoxicity (H-HT):	0.216
Drug-inuced Liver Injury (DILI):	0.95
AMES Toxicity:	0.027
Rat Oral Acute Toxicity:	0.838
Maximum Recommended Daily Dose:	0.976
Skin Sensitization:	0.921
Carcinogencity:	0.01
Eye Corrosion:	0.003
Eye Irritation:	0.878
Respiratory Toxicity:	0.913

Download Data

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

Natural Product: NPC84684

Natural Product ID:	NPC84684
*Common Name:**	Ramonanin B
IUPAC Name:	2-methoxy-4-[(1R,2'S,3S,5'R,6R)-1,3,5'-tris(4-hydroxy-3-methoxyphenyl)-3'-methylidenespiro[3,4,5,7-tetrahydro-1H-2-benzofuran-6,4'-oxolane]-2'-yl]phenol
Synonyms:	Ramonanin B
Standard InCHIKey:	GVLSMMAPMUCRRO-RZTCZVRSSA-N
Standard InCHI:	InChI=1S/C40H40O10/c1-21-36(22-6-10-28(41)32(16-22)45-2)50-39(25-9-13-31(44)35(19-25)48-5)40(21)15-14-26-27(20-40)38(24-8-12-30(43)34(18-24)47-4)49-37(26)23-7-11-29(42)33(17-23)46-3/h6-13,16-19,36-39,41-44H,1,14-15,20H2,2-5H3/t36-,37+,38-,39-,40-/m1/s1
SMILES:	COc1cc(ccc1O)[C@H]1O[C@H](C2=C1C[C@@]1(CC2)[C@H](O[C@H](C1=C)c1ccc(c(c1)OC)O)c1ccc(c(c1)OC)O)c1ccc(c(c1)OC)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL1782126
PubChem CID:	53327876
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
NPO30469	Guaiacum sanctum	Species	Zygophyllaceae	Eukaryota	n.a.	heartwood	n.a.	PMID[21391655]
NPO1570	Guaiacum officinale	Species	Zygophyllaceae	Eukaryota	n.a.	heartwood	n.a.	PMID[21391655]
NPO1570	Guaiacum officinale	Species	Zygophyllaceae	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
Others	1

Activity Type	# Activity
Cell Line	2

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT82	Cell Line	MDA-MB-231	Homo sapiens	IC50	=	18000.0	nM	PMID[476387]
NPT82	Cell Line	MDA-MB-231	Homo sapiens	Activity	<	4.0	%	PMID[476387]

☑ 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 NPC84684 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	442
0.1-0.2	1364
0.2-0.3	3585
0.3-0.4	9777
0.4-0.5	9503
0.5-0.6	6014
0.6-0.7	8922
0.7-0.8	2687
0.8-0.85	341
0.85-0.9	56
0.9-0.95	2
0.95-1	4

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC238216
1.0	High Similarity	NPC185388
1.0	High Similarity	NPC208994
0.9078	High Similarity	NPC470372
0.8936	High Similarity	NPC260842
0.8794	High Similarity	NPC77861
0.8786	High Similarity	NPC471942
0.8776	High Similarity	NPC304048
0.8776	High Similarity	NPC226153
0.8723	High Similarity	NPC93783
0.8716	High Similarity	NPC473266
0.8716	High Similarity	NPC470826
0.8716	High Similarity	NPC470098
0.8643	High Similarity	NPC4940
0.8639	High Similarity	NPC241846
0.8639	High Similarity	NPC93610
0.8623	High Similarity	NPC45774
0.8623	High Similarity	NPC282703
0.8623	High Similarity	NPC11258
0.8623	High Similarity	NPC21867
0.8623	High Similarity	NPC129570
0.8623	High Similarity	NPC128208
0.8623	High Similarity	NPC184733
0.8611	High Similarity	NPC55793
0.8611	High Similarity	NPC262189
0.86	High Similarity	NPC321972
0.86	High Similarity	NPC329343
0.86	High Similarity	NPC324517
0.8571	High Similarity	NPC158079
0.8571	High Similarity	NPC228346
0.8571	High Similarity	NPC161557
0.8571	High Similarity	NPC27843
0.8571	High Similarity	NPC115207
0.8571	High Similarity	NPC7171
0.8571	High Similarity	NPC40432
0.8553	High Similarity	NPC157333
0.8533	High Similarity	NPC477612
0.8523	High Similarity	NPC281549
0.8511	High Similarity	NPC207400
0.8511	High Similarity	NPC181049
0.8503	High Similarity	NPC470097
0.8503	High Similarity	NPC471415
0.8503	High Similarity	NPC114119
0.85	High Similarity	NPC257582
0.85	High Similarity	NPC242807
0.85	High Similarity	NPC241522
0.85	High Similarity	NPC174495
0.85	High Similarity	NPC153739
0.85	High Similarity	NPC145305
0.85	High Similarity	NPC42300
0.85	High Similarity	NPC92164
0.85	High Similarity	NPC187998
0.85	High Similarity	NPC77040
0.85	High Similarity	NPC64201
0.8489	Intermediate Similarity	NPC474178
0.8489	Intermediate Similarity	NPC245826
0.8489	Intermediate Similarity	NPC252307
0.8487	Intermediate Similarity	NPC115203
0.8483	Intermediate Similarity	NPC22317
0.8478	Intermediate Similarity	NPC17837
0.8478	Intermediate Similarity	NPC304630
0.8472	Intermediate Similarity	NPC474390
0.8456	Intermediate Similarity	NPC328567
0.8456	Intermediate Similarity	NPC99183
0.8456	Intermediate Similarity	NPC327412
0.8456	Intermediate Similarity	NPC320671
0.8456	Intermediate Similarity	NPC262297
0.8456	Intermediate Similarity	NPC320970
0.8446	Intermediate Similarity	NPC473909
0.8446	Intermediate Similarity	NPC274960
0.8446	Intermediate Similarity	NPC143120
0.844	Intermediate Similarity	NPC277804
0.8429	Intermediate Similarity	NPC475875
0.84	Intermediate Similarity	NPC227516
0.84	Intermediate Similarity	NPC20757
0.8394	Intermediate Similarity	NPC471693
0.8392	Intermediate Similarity	NPC193026
0.8392	Intermediate Similarity	NPC187616
0.8392	Intermediate Similarity	NPC49603
0.8389	Intermediate Similarity	NPC324492
0.8389	Intermediate Similarity	NPC260397
0.8389	Intermediate Similarity	NPC317053
0.8378	Intermediate Similarity	NPC28440
0.8378	Intermediate Similarity	NPC171932
0.8377	Intermediate Similarity	NPC202104
0.8367	Intermediate Similarity	NPC472087
0.8367	Intermediate Similarity	NPC472088
0.8367	Intermediate Similarity	NPC302506
0.8367	Intermediate Similarity	NPC67467
0.8357	Intermediate Similarity	NPC470084
0.8356	Intermediate Similarity	NPC106055
0.8356	Intermediate Similarity	NPC266197
0.8356	Intermediate Similarity	NPC472092
0.8356	Intermediate Similarity	NPC472091
0.8356	Intermediate Similarity	NPC291101
0.8356	Intermediate Similarity	NPC472090
0.8356	Intermediate Similarity	NPC110699
0.8345	Intermediate Similarity	NPC58607
0.8345	Intermediate Similarity	NPC178284
0.8345	Intermediate Similarity	NPC191037
0.8344	Intermediate Similarity	NPC321657
0.8344	Intermediate Similarity	NPC318373
0.8344	Intermediate Similarity	NPC211561
0.8333	Intermediate Similarity	NPC141765
0.8333	Intermediate Similarity	NPC99572
0.8333	Intermediate Similarity	NPC126409
0.8333	Intermediate Similarity	NPC24490
0.8333	Intermediate Similarity	NPC135777
0.8333	Intermediate Similarity	NPC142547
0.8333	Intermediate Similarity	NPC34103
0.8333	Intermediate Similarity	NPC165155
0.8322	Intermediate Similarity	NPC272619
0.8322	Intermediate Similarity	NPC158331
0.8322	Intermediate Similarity	NPC286245
0.8322	Intermediate Similarity	NPC307205
0.8322	Intermediate Similarity	NPC181615
0.8311	Intermediate Similarity	NPC477898
0.831	Intermediate Similarity	NPC470096
0.831	Intermediate Similarity	NPC470095
0.8301	Intermediate Similarity	NPC476391
0.8299	Intermediate Similarity	NPC472089
0.8299	Intermediate Similarity	NPC472711
0.8298	Intermediate Similarity	NPC86030
0.8298	Intermediate Similarity	NPC5851
0.8289	Intermediate Similarity	NPC145527
0.8289	Intermediate Similarity	NPC470619
0.8289	Intermediate Similarity	NPC470618
0.8289	Intermediate Similarity	NPC208785
0.8288	Intermediate Similarity	NPC22517
0.8286	Intermediate Similarity	NPC41706
0.8286	Intermediate Similarity	NPC118533
0.8286	Intermediate Similarity	NPC111247
0.8286	Intermediate Similarity	NPC183181
0.8286	Intermediate Similarity	NPC118787
0.8286	Intermediate Similarity	NPC147821
0.8286	Intermediate Similarity	NPC165045
0.8286	Intermediate Similarity	NPC163332
0.8286	Intermediate Similarity	NPC292056
0.8286	Intermediate Similarity	NPC319625
0.8278	Intermediate Similarity	NPC102934
0.8278	Intermediate Similarity	NPC252402
0.8276	Intermediate Similarity	NPC177160
0.8276	Intermediate Similarity	NPC52277
0.8276	Intermediate Similarity	NPC68292
0.8276	Intermediate Similarity	NPC29799
0.8276	Intermediate Similarity	NPC209985
0.8276	Intermediate Similarity	NPC263367
0.8276	Intermediate Similarity	NPC10737
0.8276	Intermediate Similarity	NPC177035
0.8276	Intermediate Similarity	NPC477939
0.8276	Intermediate Similarity	NPC199459
0.8276	Intermediate Similarity	NPC471988
0.8276	Intermediate Similarity	NPC156502
0.8276	Intermediate Similarity	NPC54743
0.8273	Intermediate Similarity	NPC194519
0.8273	Intermediate Similarity	NPC148627
0.8269	Intermediate Similarity	NPC125495
0.8269	Intermediate Similarity	NPC470827
0.8267	Intermediate Similarity	NPC126291
0.8264	Intermediate Similarity	NPC311256
0.8264	Intermediate Similarity	NPC244983
0.8264	Intermediate Similarity	NPC287745
0.8264	Intermediate Similarity	NPC326095
0.8264	Intermediate Similarity	NPC67247
0.8261	Intermediate Similarity	NPC317769
0.8261	Intermediate Similarity	NPC31344
0.8255	Intermediate Similarity	NPC304894
0.8255	Intermediate Similarity	NPC471065
0.8255	Intermediate Similarity	NPC84181
0.8255	Intermediate Similarity	NPC15659
0.8255	Intermediate Similarity	NPC253015
0.8255	Intermediate Similarity	NPC179521
0.8252	Intermediate Similarity	NPC474134
0.8252	Intermediate Similarity	NPC201587
0.8252	Intermediate Similarity	NPC253105
0.8252	Intermediate Similarity	NPC204215
0.8252	Intermediate Similarity	NPC303144
0.8252	Intermediate Similarity	NPC471505
0.8252	Intermediate Similarity	NPC175067
0.8252	Intermediate Similarity	NPC131128
0.8243	Intermediate Similarity	NPC476356
0.8239	Intermediate Similarity	NPC143483
0.8235	Intermediate Similarity	NPC125823
0.8235	Intermediate Similarity	NPC143480
0.8235	Intermediate Similarity	NPC7145
0.8235	Intermediate Similarity	NPC85192
0.8228	Intermediate Similarity	NPC7191
0.8228	Intermediate Similarity	NPC149873
0.8227	Intermediate Similarity	NPC307050
0.8227	Intermediate Similarity	NPC277458
0.8227	Intermediate Similarity	NPC72529
0.8224	Intermediate Similarity	NPC475250
0.8224	Intermediate Similarity	NPC476969
0.8219	Intermediate Similarity	NPC281780
0.8217	Intermediate Similarity	NPC470828
0.8214	Intermediate Similarity	NPC206882
0.8214	Intermediate Similarity	NPC156854
0.8214	Intermediate Similarity	NPC134431
0.8212	Intermediate Similarity	NPC202742
0.8212	Intermediate Similarity	NPC70409

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 NPC84684 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	338
0.1-0.2	852
0.2-0.3	1697
0.3-0.4	2852
0.4-0.5	1807
0.5-0.6	1069
0.6-0.7	481
0.7-0.8	53
0.8-0.85	1
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8169	Intermediate Similarity	NPD3027	Phase 3
0.8	Intermediate Similarity	NPD3619	Clinical (unspecified phase)
0.8	Intermediate Similarity	NPD3620	Phase 2
0.7755	Intermediate Similarity	NPD1613	Approved
0.7755	Intermediate Similarity	NPD1612	Clinical (unspecified phase)
0.7654	Intermediate Similarity	NPD6234	Discontinued
0.7651	Intermediate Similarity	NPD7228	Approved
0.7613	Intermediate Similarity	NPD6143	Clinical (unspecified phase)
0.7603	Intermediate Similarity	NPD1529	Clinical (unspecified phase)
0.7584	Intermediate Similarity	NPD5735	Approved
0.7574	Intermediate Similarity	NPD228	Approved
0.7534	Intermediate Similarity	NPD1530	Clinical (unspecified phase)
0.7532	Intermediate Similarity	NPD8166	Discontinued
0.7471	Intermediate Similarity	NPD8397	Clinical (unspecified phase)
0.7464	Intermediate Similarity	NPD5283	Phase 1
0.7455	Intermediate Similarity	NPD8127	Discontinued
0.7451	Intermediate Similarity	NPD7266	Discontinued
0.7448	Intermediate Similarity	NPD8651	Approved
0.7423	Intermediate Similarity	NPD4965	Approved
0.7423	Intermediate Similarity	NPD4967	Phase 2
0.7423	Intermediate Similarity	NPD4966	Approved
0.7415	Intermediate Similarity	NPD2861	Phase 2
0.7399	Intermediate Similarity	NPD8055	Clinical (unspecified phase)
0.7394	Intermediate Similarity	NPD1357	Approved
0.7383	Intermediate Similarity	NPD4907	Clinical (unspecified phase)
0.7379	Intermediate Similarity	NPD4379	Clinical (unspecified phase)
0.7365	Intermediate Similarity	NPD4908	Phase 1
0.7361	Intermediate Similarity	NPD3705	Approved
0.7357	Intermediate Similarity	NPD7157	Approved
0.7355	Intermediate Similarity	NPD6674	Discontinued
0.7346	Intermediate Similarity	NPD37	Approved
0.7342	Intermediate Similarity	NPD4160	Clinical (unspecified phase)
0.7321	Intermediate Similarity	NPD6167	Clinical (unspecified phase)
0.7321	Intermediate Similarity	NPD6166	Phase 2
0.7321	Intermediate Similarity	NPD6168	Clinical (unspecified phase)
0.7314	Intermediate Similarity	NPD7906	Approved
0.7283	Intermediate Similarity	NPD7312	Approved
0.7283	Intermediate Similarity	NPD7310	Approved
0.7283	Intermediate Similarity	NPD7311	Approved
0.7283	Intermediate Similarity	NPD7313	Approved
0.7273	Intermediate Similarity	NPD7832	Clinical (unspecified phase)
0.7273	Intermediate Similarity	NPD7833	Phase 2
0.7273	Intermediate Similarity	NPD7831	Phase 2
0.7266	Intermediate Similarity	NPD7843	Approved
0.726	Intermediate Similarity	NPD5327	Phase 3
0.7241	Intermediate Similarity	NPD7309	Approved
0.7237	Intermediate Similarity	NPD3657	Discovery
0.7219	Intermediate Similarity	NPD27	Approved
0.7219	Intermediate Similarity	NPD2489	Approved
0.7212	Intermediate Similarity	NPD4868	Clinical (unspecified phase)
0.72	Intermediate Similarity	NPD7095	Approved
0.7195	Intermediate Similarity	NPD8455	Phase 2
0.719	Intermediate Similarity	NPD6353	Approved
0.7174	Intermediate Similarity	NPD3022	Approved
0.7174	Intermediate Similarity	NPD3021	Approved
0.7171	Intermediate Similarity	NPD1558	Phase 1
0.7168	Intermediate Similarity	NPD7240	Approved
0.7162	Intermediate Similarity	NPD3094	Phase 2
0.716	Intermediate Similarity	NPD2969	Approved
0.716	Intermediate Similarity	NPD2970	Approved
0.7152	Intermediate Similarity	NPD6410	Clinical (unspecified phase)
0.7143	Intermediate Similarity	NPD2982	Phase 2
0.7143	Intermediate Similarity	NPD7097	Phase 1
0.7143	Intermediate Similarity	NPD2983	Phase 2
0.7134	Intermediate Similarity	NPD4236	Phase 3
0.7134	Intermediate Similarity	NPD4237	Approved
0.7134	Intermediate Similarity	NPD1934	Approved
0.7134	Intermediate Similarity	NPD5698	Clinical (unspecified phase)
0.7123	Intermediate Similarity	NPD3092	Approved
0.7114	Intermediate Similarity	NPD6584	Phase 3
0.711	Intermediate Similarity	NPD7993	Clinical (unspecified phase)
0.7101	Intermediate Similarity	NPD3051	Approved
0.7097	Intermediate Similarity	NPD5588	Approved
0.7095	Intermediate Similarity	NPD6696	Suspended
0.7091	Intermediate Similarity	NPD6818	Clinical (unspecified phase)
0.7091	Intermediate Similarity	NPD2393	Clinical (unspecified phase)
0.7089	Intermediate Similarity	NPD4109	Clinical (unspecified phase)
0.7089	Intermediate Similarity	NPD4110	Phase 3
0.7075	Intermediate Similarity	NPD2981	Phase 2
0.707	Intermediate Similarity	NPD7037	Approved
0.7067	Intermediate Similarity	NPD3018	Phase 2
0.7059	Intermediate Similarity	NPD4060	Phase 1
0.7059	Intermediate Similarity	NPD4140	Approved
0.7052	Intermediate Similarity	NPD7074	Phase 3
0.7041	Intermediate Similarity	NPD7199	Phase 2
0.7032	Intermediate Similarity	NPD4537	Clinical (unspecified phase)
0.7032	Intermediate Similarity	NPD4536	Approved
0.7032	Intermediate Similarity	NPD4538	Approved
0.7025	Intermediate Similarity	NPD3060	Approved
0.7012	Intermediate Similarity	NPD7028	Phase 2
0.7006	Intermediate Similarity	NPD2029	Clinical (unspecified phase)
0.7	Intermediate Similarity	NPD4624	Approved
0.7	Intermediate Similarity	NPD6917	Clinical (unspecified phase)
0.7	Intermediate Similarity	NPD5058	Phase 3
0.6994	Remote Similarity	NPD7054	Approved
0.6989	Remote Similarity	NPD7680	Approved
0.6989	Remote Similarity	NPD4578	Approved
0.6989	Remote Similarity	NPD4577	Approved
0.6988	Remote Similarity	NPD2977	Approved
0.6988	Remote Similarity	NPD2978	Approved
0.6986	Remote Similarity	NPD5846	Approved
0.6986	Remote Similarity	NPD6516	Phase 2
0.6981	Remote Similarity	NPD4628	Phase 3
0.6981	Remote Similarity	NPD6331	Phase 2
0.6978	Remote Similarity	NPD2684	Approved
0.6966	Remote Similarity	NPD4663	Approved
0.6966	Remote Similarity	NPD3091	Approved
0.6959	Remote Similarity	NPD7184	Clinical (unspecified phase)
0.6954	Remote Similarity	NPD7472	Approved
0.6949	Remote Similarity	NPD8054	Approved
0.6949	Remote Similarity	NPD8053	Approved
0.6937	Remote Similarity	NPD6190	Approved
0.6936	Remote Similarity	NPD3818	Discontinued
0.6928	Remote Similarity	NPD6798	Discontinued
0.6928	Remote Similarity	NPD7945	Clinical (unspecified phase)
0.6914	Remote Similarity	NPD7004	Clinical (unspecified phase)
0.6913	Remote Similarity	NPD6583	Phase 3
0.6913	Remote Similarity	NPD6582	Phase 2
0.6913	Remote Similarity	NPD3600	Clinical (unspecified phase)
0.6905	Remote Similarity	NPD3882	Suspended
0.6901	Remote Similarity	NPD6232	Discontinued
0.6899	Remote Similarity	NPD5763	Approved
0.6899	Remote Similarity	NPD1375	Discontinued
0.6899	Remote Similarity	NPD5762	Approved
0.6897	Remote Similarity	NPD5844	Phase 1
0.6897	Remote Similarity	NPD5536	Phase 2
0.6892	Remote Similarity	NPD1610	Phase 2
0.689	Remote Similarity	NPD1653	Approved
0.6886	Remote Similarity	NPD2801	Approved
0.6883	Remote Similarity	NPD6233	Phase 2
0.6879	Remote Similarity	NPD5960	Phase 3
0.6879	Remote Similarity	NPD7473	Discontinued
0.6875	Remote Similarity	NPD7685	Pre-registration
0.6875	Remote Similarity	NPD6671	Approved
0.6871	Remote Similarity	NPD5261	Clinical (unspecified phase)
0.6865	Remote Similarity	NPD7237	Clinical (unspecified phase)
0.6863	Remote Similarity	NPD4625	Phase 3
0.6854	Remote Similarity	NPD7090	Clinical (unspecified phase)
0.6849	Remote Similarity	NPD1548	Phase 1
0.6848	Remote Similarity	NPD6055	Clinical (unspecified phase)
0.6845	Remote Similarity	NPD6374	Clinical (unspecified phase)
0.6845	Remote Similarity	NPD2560	Approved
0.6845	Remote Similarity	NPD2563	Approved
0.6842	Remote Similarity	NPD5736	Approved
0.6842	Remote Similarity	NPD6959	Discontinued
0.6839	Remote Similarity	NPD5837	Clinical (unspecified phase)
0.6836	Remote Similarity	NPD7808	Phase 3
0.6835	Remote Similarity	NPD2161	Phase 2
0.6829	Remote Similarity	NPD6980	Clinical (unspecified phase)
0.6826	Remote Similarity	NPD5722	Discontinued
0.681	Remote Similarity	NPD7447	Phase 1
0.681	Remote Similarity	NPD7422	Clinical (unspecified phase)
0.681	Remote Similarity	NPD7446	Clinical (unspecified phase)
0.681	Remote Similarity	NPD4123	Phase 3
0.6809	Remote Similarity	NPD5451	Approved
0.6807	Remote Similarity	NPD4380	Phase 2
0.6805	Remote Similarity	NPD7773	Phase 2
0.6802	Remote Similarity	NPD6071	Discontinued
0.68	Remote Similarity	NPD4749	Approved
0.6798	Remote Similarity	NPD8313	Approved
0.6798	Remote Similarity	NPD8312	Approved
0.6797	Remote Similarity	NPD5752	Clinical (unspecified phase)
0.6795	Remote Similarity	NPD6355	Discontinued
0.679	Remote Similarity	NPD6783	Clinical (unspecified phase)
0.6786	Remote Similarity	NPD5773	Approved
0.6786	Remote Similarity	NPD5772	Approved
0.678	Remote Similarity	NPD7251	Discontinued
0.6774	Remote Similarity	NPD2674	Phase 3
0.6774	Remote Similarity	NPD6663	Approved
0.6768	Remote Similarity	NPD6273	Approved
0.6765	Remote Similarity	NPD7975	Clinical (unspecified phase)
0.6757	Remote Similarity	NPD3095	Discontinued
0.6757	Remote Similarity	NPD5126	Approved
0.6757	Remote Similarity	NPD5125	Phase 3
0.6752	Remote Similarity	NPD4097	Suspended
0.6748	Remote Similarity	NPD7040	Clinical (unspecified phase)
0.6748	Remote Similarity	NPD7213	Phase 3
0.6748	Remote Similarity	NPD7212	Phase 2
0.6748	Remote Similarity	NPD7041	Phase 2
0.6747	Remote Similarity	NPD7458	Discontinued
0.6746	Remote Similarity	NPD8443	Clinical (unspecified phase)
0.6736	Remote Similarity	NPD4869	Clinical (unspecified phase)
0.6735	Remote Similarity	NPD7741	Discontinued
0.6728	Remote Similarity	NPD5241	Discontinued
0.6728	Remote Similarity	NPD5307	Clinical (unspecified phase)
0.6724	Remote Similarity	NPD4481	Phase 3
0.6723	Remote Similarity	NPD6797	Phase 2
0.6714	Remote Similarity	NPD968	Approved
0.671	Remote Similarity	NPD6812	Clinical (unspecified phase)
0.6709	Remote Similarity	NPD6895	Approved
0.6709	Remote Similarity	NPD6896	Approved
0.6708	Remote Similarity	NPD5177	Phase 3
0.6708	Remote Similarity	NPD4162	Approved
0.6706	Remote Similarity	NPD7768	Phase 2
0.6687	Remote Similarity	NPD3687	Approved
0.6687	Remote Similarity	NPD3686	Approved
0.6687	Remote Similarity	NPD7124	Phase 2
0.6686	Remote Similarity	NPD5494	Approved
0.6685	Remote Similarity	NPD6559	Discontinued
0.6667	Remote Similarity	NPD7003	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