NPASS Compound

Structure

CID40728 OpenBabel06191715372D 43 45 0 0 1 0 0 0 0 0999 V2000 3.3923 -1.1080 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9345 1.0827 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2617 4.0827 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9345 2.8147 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5296 3.0827 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8005 -0.4173 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8005 -1.4173 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0238 -2.3328 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4345 1.9487 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4141 -1.3159 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9345 1.0827 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3956 4.5827 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7450 -0.5727 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.4345 1.9487 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9345 1.0827 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3364 2.5827 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0685 2.5827 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.4345 1.9487 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5296 4.0827 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -2.9345 0.0827 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.9345 -1.9173 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3546 -1.5897 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2024 3.0827 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.3364 1.5827 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0685 1.5827 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.0540 0.3783 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0685 -0.4173 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.2024 0.0827 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.3364 4.5827 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4067 0.9135 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.9945 0.1045 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.9345 1.0827 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.2024 1.0827 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.9345 -2.9173 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.3765 -1.7976 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.0322 0.5862 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.3364 -0.4173 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.3364 5.5827 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.0685 -1.4173 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.6637 -0.6386 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.2024 4.0827 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.3849 1.1215 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 10 1 0 0 0 0 2 11 2 0 0 0 0 3 12 1 0 0 0 0 4 18 2 0 0 0 0 5 19 1 0 0 0 0 6 20 1 0 0 0 0 7 21 1 0 0 0 0 8 22 1 0 0 0 0 10 13 1 0 0 0 0 11 18 1 0 0 0 0 12 19 1 0 0 0 0 13 26 1 0 0 0 0 14 15 1 0 0 0 0 14 18 1 0 0 0 0 15 32 1 0 0 0 0 16 23 1 0 0 0 0 16 24 2 0 0 0 0 17 23 1 0 0 0 0 17 25 1 0 0 0 0 19 29 1 0 0 0 0 20 27 1 0 0 0 0 20 32 1 6 0 0 0 21 34 2 0 0 0 0 21 39 1 0 0 0 0 22 35 2 0 0 0 0 22 40 1 0 0 0 0 23 41 1 6 0 0 0 24 30 1 0 0 0 0 25 32 1 1 0 0 0 25 33 1 0 0 0 0 26 36 2 0 0 0 0 26 42 1 0 0 0 0 27 28 1 0 0 0 0 27 39 1 6 0 0 0 28 33 1 6 0 0 0 28 37 1 0 0 0 0 29 38 2 0 0 0 0 29 41 1 0 0 0 0 30 42 1 6 0 0 0 30 43 1 0 0 0 0 31 33 1 6 0 0 0 31 40 1 0 0 0 0 31 43 1 0 0 0 0 32 9 1 1 0 0 0 33 24 1 1 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	604.32
Volume:	623.102
LogP:	4.286
LogD:	3.411
LogS:	-4.605
# Rotatable Bonds:	16
TPSA:	134.66
# H-Bond Aceptor:	10
# H-Bond Donor:	1
# Rings:	3
# Heavy Atoms:	10

MedChem Properties

QED Drug-Likeness Score:	0.141
Synthetic Accessibility Score:	6.003
Fsp3:	0.697
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.844
MDCK Permeability:	7.037552131805569e-05
Pgp-inhibitor:	0.998
Pgp-substrate:	0.035
Human Intestinal Absorption (HIA):	0.006
20% Bioavailability (F20%):	0.006
30% Bioavailability (F30%):	0.447

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.065
Plasma Protein Binding (PPB):	79.61553955078125%
Volume Distribution (VD):	2.017
Pgp-substrate:	17.451303482055664%

ADMET: Metabolism

CYP1A2-inhibitor:	0.044
CYP1A2-substrate:	0.053
CYP2C19-inhibitor:	0.03
CYP2C19-substrate:	0.157
CYP2C9-inhibitor:	0.374
CYP2C9-substrate:	0.055
CYP2D6-inhibitor:	0.016
CYP2D6-substrate:	0.083
CYP3A4-inhibitor:	0.788
CYP3A4-substrate:	0.386

ADMET: Excretion

Clearance (CL):	3.589
Half-life (T1/2):	0.252

ADMET: Toxicity

hERG Blockers:	0.205
Human Hepatotoxicity (H-HT):	0.97
Drug-inuced Liver Injury (DILI):	0.969
AMES Toxicity:	0.486
Rat Oral Acute Toxicity:	0.881
Maximum Recommended Daily Dose:	0.97
Skin Sensitization:	0.755
Carcinogencity:	0.054
Eye Corrosion:	0.003
Eye Irritation:	0.011
Respiratory Toxicity:	0.943

Download Data

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

Natural Product: NPC40728

Natural Product ID:	NPC40728
*Common Name:**	Caseamembrin D
IUPAC Name:	[(1R,3S,5S,6aR,7R,8R,9R,10S,10aR)-1,9-diacetyloxy-3-butanoyloxy-10-hydroxy-7,8-dimethyl-7-(3-methylidenepent-4-enyl)-1,3,5,6,6a,8,9,10-octahydrobenzo[d][2]benzofuran-5-yl] 2-methylbutanoate
Synonyms:	Caseamembrin D
Standard InCHIKey:	ZWHARZIRGKBMPI-VHLLSUOMSA-N
Standard InCHI:	InChI=1S/C33H48O10/c1-10-13-26(36)42-30-24-16-23(41-29(38)19(5)12-3)17-25-32(9,15-14-18(4)11-2)20(6)27(39-21(7)34)28(37)33(24,25)31(43-30)40-22(8)35/h11,16,19-20,23,25,27-28,30-31,37H,2,4,10,12-15,17H2,1,3,5-9H3/t19?,20-,23+,25+,27+,28+,30+,31-,32-,33-/m0/s1
SMILES:	CCCC(=O)O[C@H]1C2=C[C@H](C[C@@H]3[C@@](C)(CCC(=C)C=C)[C@@H](C)[C@H]([C@H]([C@]23[C@@H](OC(=O)C)O1)O)OC(=O)C)OC(=O)C(C)CC
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL510107
PubChem CID:	11192734
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001551] Diterpenoids [CHEMONTID:0001757] Colensane and clerodane diterpenoids

*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
NPO24498	Casearia membranacea	Species	Salicaceae	Eukaryota	n.a.	twig	n.a.	PMID[14709876]
NPO24498	Casearia membranacea	Species	Salicaceae	Eukaryota	n.a.	leaf	n.a.	PMID[14709876]
NPO24498	Casearia membranacea	Species	Salicaceae	Eukaryota	Leaves; Twigs	n.a.	n.a.	PMID[15043402]
NPO24498	Casearia membranacea	Species	Salicaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[16309320]
NPO24498	Casearia membranacea	Species	Salicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO24498	Casearia membranacea	Species	Salicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO24498	Casearia membranacea	Species	Salicaceae	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
IC50	2

Activity Type	# Activity
Cell Line	3
NON-MOLECULAR	2

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT306	Cell Line	PC-3	Homo sapiens	IC50	=	2400.0	nM	PMID[489674]
NPT579	Cell Line	DLD-1	Homo sapiens	ED50	=	1.81	ug ml-1	PMID[489675]
NPT91	Cell Line	KB	Homo sapiens	ED50	=	5.57	ug ml-1	PMID[489675]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	IC50	=	1900.0	nM	PMID[489674]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	ED50	=	2.42	ug ml-1	PMID[489675]

☑ 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 NPC40728 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	197
0.1-0.2	1137
0.2-0.3	3931
0.3-0.4	7400
0.4-0.5	12943
0.5-0.6	8121
0.6-0.7	5813
0.7-0.8	2901
0.8-0.85	159
0.85-0.9	21
0.9-0.95	57
0.95-1	17

Similarity Score	Similarity Level	Natural Product ID
0.99	High Similarity	NPC217921
0.99	High Similarity	NPC128795
0.99	High Similarity	NPC48548
0.99	High Similarity	NPC135015
0.9802	High Similarity	NPC316974
0.98	High Similarity	NPC88013
0.98	High Similarity	NPC125423
0.9703	High Similarity	NPC311223
0.9515	High Similarity	NPC119550
0.95	High Similarity	NPC475889
0.95	High Similarity	NPC7644
0.95	High Similarity	NPC127933
0.95	High Similarity	NPC7613
0.9406	High Similarity	NPC81567
0.9406	High Similarity	NPC201880
0.9406	High Similarity	NPC264867
0.9406	High Similarity	NPC470321
0.9406	High Similarity	NPC473207
0.94	High Similarity	NPC238397
0.94	High Similarity	NPC471363
0.9333	High Similarity	NPC317460
0.9333	High Similarity	NPC321272
0.9333	High Similarity	NPC328074
0.9333	High Similarity	NPC470025
0.9327	High Similarity	NPC316708
0.9307	High Similarity	NPC134270
0.9245	High Similarity	NPC470027
0.9238	High Similarity	NPC17791
0.9238	High Similarity	NPC470026
0.9223	High Similarity	NPC184512
0.92	High Similarity	NPC473545
0.92	High Similarity	NPC472187
0.9126	High Similarity	NPC252296
0.91	High Similarity	NPC476800
0.91	High Similarity	NPC318917
0.91	High Similarity	NPC471366
0.91	High Similarity	NPC472186
0.9038	High Similarity	NPC109376
0.901	High Similarity	NPC473204
0.9	High Similarity	NPC472188
0.8952	High Similarity	NPC224660
0.8952	High Similarity	NPC470024
0.8942	High Similarity	NPC172867
0.89	High Similarity	NPC171598
0.88	High Similarity	NPC472189
0.88	High Similarity	NPC471362
0.88	High Similarity	NPC471372
0.8762	High Similarity	NPC218158
0.8679	High Similarity	NPC293512
0.8679	High Similarity	NPC472390
0.8667	High Similarity	NPC470768
0.8661	High Similarity	NPC470914
0.8661	High Similarity	NPC122971
0.8627	High Similarity	NPC98112
0.8624	High Similarity	NPC473125
0.8611	High Similarity	NPC83005
0.8585	High Similarity	NPC239961
0.8585	High Similarity	NPC470763
0.8585	High Similarity	NPC470767
0.8585	High Similarity	NPC82251
0.8571	High Similarity	NPC473828
0.8571	High Similarity	NPC474124
0.8571	High Similarity	NPC473617
0.8558	High Similarity	NPC198992
0.8558	High Similarity	NPC280991
0.8545	High Similarity	NPC264153
0.8545	High Similarity	NPC44298
0.8545	High Similarity	NPC473128
0.8545	High Similarity	NPC311592
0.8545	High Similarity	NPC293658
0.8545	High Similarity	NPC290608
0.8545	High Similarity	NPC40133
0.8545	High Similarity	NPC474410
0.8545	High Similarity	NPC75167
0.8545	High Similarity	NPC49413
0.8522	High Similarity	NPC41129
0.8519	High Similarity	NPC206618
0.8515	High Similarity	NPC88507
0.8496	Intermediate Similarity	NPC477071
0.8482	Intermediate Similarity	NPC473405
0.8476	Intermediate Similarity	NPC475344
0.8476	Intermediate Similarity	NPC476471
0.8476	Intermediate Similarity	NPC472552
0.8468	Intermediate Similarity	NPC181145
0.8462	Intermediate Similarity	NPC477971
0.8462	Intermediate Similarity	NPC219285
0.8462	Intermediate Similarity	NPC477972
0.8462	Intermediate Similarity	NPC477968
0.8462	Intermediate Similarity	NPC20113
0.8462	Intermediate Similarity	NPC228251
0.8462	Intermediate Similarity	NPC161527
0.8447	Intermediate Similarity	NPC309503
0.8447	Intermediate Similarity	NPC155319
0.8447	Intermediate Similarity	NPC239547
0.8447	Intermediate Similarity	NPC125551
0.8447	Intermediate Similarity	NPC96597
0.8447	Intermediate Similarity	NPC91197
0.844	Intermediate Similarity	NPC177047
0.8431	Intermediate Similarity	NPC275310
0.8431	Intermediate Similarity	NPC230347
0.8431	Intermediate Similarity	NPC286612
0.8426	Intermediate Similarity	NPC38948
0.8407	Intermediate Similarity	NPC471548
0.8396	Intermediate Similarity	NPC281378
0.8396	Intermediate Similarity	NPC23584
0.8393	Intermediate Similarity	NPC207637
0.8381	Intermediate Similarity	NPC475617
0.8381	Intermediate Similarity	NPC472554
0.8378	Intermediate Similarity	NPC473159
0.8365	Intermediate Similarity	NPC477928
0.8364	Intermediate Similarity	NPC250481
0.8364	Intermediate Similarity	NPC285410
0.8364	Intermediate Similarity	NPC263827
0.835	Intermediate Similarity	NPC311166
0.8348	Intermediate Similarity	NPC476204
0.8348	Intermediate Similarity	NPC170084
0.8333	Intermediate Similarity	NPC33053
0.8333	Intermediate Similarity	NPC473586
0.8319	Intermediate Similarity	NPC473968
0.8318	Intermediate Similarity	NPC31430
0.8318	Intermediate Similarity	NPC474550
0.8318	Intermediate Similarity	NPC473543
0.8318	Intermediate Similarity	NPC473577
0.8318	Intermediate Similarity	NPC85593
0.8318	Intermediate Similarity	NPC93352
0.8318	Intermediate Similarity	NPC475585
0.8304	Intermediate Similarity	NPC220293
0.8304	Intermediate Similarity	NPC475163
0.8302	Intermediate Similarity	NPC11956
0.8302	Intermediate Similarity	NPC470571
0.8302	Intermediate Similarity	NPC121423
0.83	Intermediate Similarity	NPC470819
0.8288	Intermediate Similarity	NPC125923
0.8288	Intermediate Similarity	NPC116794
0.8288	Intermediate Similarity	NPC174836
0.8288	Intermediate Similarity	NPC64106
0.8288	Intermediate Similarity	NPC212968
0.8288	Intermediate Similarity	NPC65590
0.8288	Intermediate Similarity	NPC231797
0.8286	Intermediate Similarity	NPC64348
0.8286	Intermediate Similarity	NPC188968
0.8286	Intermediate Similarity	NPC272223
0.8273	Intermediate Similarity	NPC108709
0.8273	Intermediate Similarity	NPC103627
0.8273	Intermediate Similarity	NPC68419
0.8273	Intermediate Similarity	NPC110139
0.8273	Intermediate Similarity	NPC274507
0.8273	Intermediate Similarity	NPC199457
0.8273	Intermediate Similarity	NPC191439
0.8273	Intermediate Similarity	NPC75747
0.8273	Intermediate Similarity	NPC129340
0.8273	Intermediate Similarity	NPC102914
0.8273	Intermediate Similarity	NPC220984
0.8273	Intermediate Similarity	NPC170974
0.8273	Intermediate Similarity	NPC101450
0.8273	Intermediate Similarity	NPC7870
0.8261	Intermediate Similarity	NPC48692
0.8257	Intermediate Similarity	NPC38376
0.8257	Intermediate Similarity	NPC475263
0.8257	Intermediate Similarity	NPC80210
0.8246	Intermediate Similarity	NPC470515
0.8246	Intermediate Similarity	NPC45475
0.8241	Intermediate Similarity	NPC470055
0.8241	Intermediate Similarity	NPC475290
0.8241	Intermediate Similarity	NPC470056
0.823	Intermediate Similarity	NPC471816
0.8224	Intermediate Similarity	NPC473124
0.8224	Intermediate Similarity	NPC120009
0.8224	Intermediate Similarity	NPC473523
0.8224	Intermediate Similarity	NPC473123
0.8218	Intermediate Similarity	NPC471371
0.8218	Intermediate Similarity	NPC470817
0.8218	Intermediate Similarity	NPC471370
0.8214	Intermediate Similarity	NPC251309
0.8214	Intermediate Similarity	NPC144068
0.8214	Intermediate Similarity	NPC271138
0.8214	Intermediate Similarity	NPC269315
0.8208	Intermediate Similarity	NPC476132
0.8198	Intermediate Similarity	NPC297208
0.8198	Intermediate Similarity	NPC30397
0.8198	Intermediate Similarity	NPC190837
0.8198	Intermediate Similarity	NPC211798
0.8198	Intermediate Similarity	NPC191763
0.8198	Intermediate Similarity	NPC65034
0.8198	Intermediate Similarity	NPC473481
0.8198	Intermediate Similarity	NPC235841
0.8198	Intermediate Similarity	NPC292196
0.8198	Intermediate Similarity	NPC208189
0.8198	Intermediate Similarity	NPC179434
0.8198	Intermediate Similarity	NPC108748
0.819	Intermediate Similarity	NPC473154
0.8182	Intermediate Similarity	NPC204407
0.8182	Intermediate Similarity	NPC221110
0.8182	Intermediate Similarity	NPC180459
0.8182	Intermediate Similarity	NPC173905
0.8182	Intermediate Similarity	NPC257853
0.8182	Intermediate Similarity	NPC195116
0.8182	Intermediate Similarity	NPC157530
0.8182	Intermediate Similarity	NPC143706
0.8182	Intermediate Similarity	NPC265655

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 NPC40728 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	165
0.1-0.2	1372
0.2-0.3	3683
0.3-0.4	2511
0.4-0.5	890
0.5-0.6	321
0.6-0.7	183
0.7-0.8	25
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
0.8091	Intermediate Similarity	NPD6686	Approved
0.7881	Intermediate Similarity	NPD8517	Approved
0.7881	Intermediate Similarity	NPD8513	Phase 3
0.7881	Intermediate Similarity	NPD7503	Approved
0.7881	Intermediate Similarity	NPD8516	Approved
0.7881	Intermediate Similarity	NPD8515	Approved
0.7881	Intermediate Similarity	NPD8033	Approved
0.7863	Intermediate Similarity	NPD7516	Approved
0.7857	Intermediate Similarity	NPD8132	Clinical (unspecified phase)
0.7797	Intermediate Similarity	NPD8294	Approved
0.7797	Intermediate Similarity	NPD8377	Approved
0.7778	Intermediate Similarity	NPD7327	Approved
0.7778	Intermediate Similarity	NPD7328	Approved
0.7731	Intermediate Similarity	NPD8335	Approved
0.7731	Intermediate Similarity	NPD8378	Approved
0.7731	Intermediate Similarity	NPD8379	Approved
0.7731	Intermediate Similarity	NPD8380	Approved
0.7731	Intermediate Similarity	NPD8296	Approved
0.7685	Intermediate Similarity	NPD4225	Approved
0.7623	Intermediate Similarity	NPD7507	Approved
0.7586	Intermediate Similarity	NPD8133	Approved
0.7523	Intermediate Similarity	NPD7638	Approved
0.7455	Intermediate Similarity	NPD7639	Approved
0.7455	Intermediate Similarity	NPD7640	Approved
0.744	Intermediate Similarity	NPD7319	Approved
0.7395	Intermediate Similarity	NPD8295	Clinical (unspecified phase)
0.7391	Intermediate Similarity	NPD4061	Clinical (unspecified phase)
0.7387	Intermediate Similarity	NPD5344	Discontinued
0.7368	Intermediate Similarity	NPD6412	Phase 2
0.7364	Intermediate Similarity	NPD8029	Clinical (unspecified phase)
0.7358	Intermediate Similarity	NPD7838	Discovery
0.7317	Intermediate Similarity	NPD8328	Phase 3
0.728	Intermediate Similarity	NPD8074	Phase 3
0.7265	Intermediate Similarity	NPD8413	Clinical (unspecified phase)
0.7222	Intermediate Similarity	NPD7736	Approved
0.7179	Intermediate Similarity	NPD5955	Clinical (unspecified phase)
0.7143	Intermediate Similarity	NPD8293	Discontinued
0.7143	Intermediate Similarity	NPD6648	Approved
0.7107	Intermediate Similarity	NPD7115	Discovery
0.7097	Intermediate Similarity	NPD6370	Approved
0.7037	Intermediate Similarity	NPD46	Approved
0.7037	Intermediate Similarity	NPD6698	Approved
0.7009	Intermediate Similarity	NPD5345	Clinical (unspecified phase)
0.6984	Remote Similarity	NPD7492	Approved
0.6972	Remote Similarity	NPD7983	Approved
0.6972	Remote Similarity	NPD7637	Suspended
0.6952	Remote Similarity	NPD6400	Clinical (unspecified phase)
0.6935	Remote Similarity	NPD6054	Approved
0.6929	Remote Similarity	NPD6616	Approved
0.6923	Remote Similarity	NPD5954	Clinical (unspecified phase)
0.6917	Remote Similarity	NPD8297	Approved
0.6917	Remote Similarity	NPD6882	Approved
0.6909	Remote Similarity	NPD5779	Approved
0.6909	Remote Similarity	NPD5778	Approved
0.6875	Remote Similarity	NPD7078	Approved
0.687	Remote Similarity	NPD7632	Discontinued
0.6829	Remote Similarity	NPD6009	Approved
0.68	Remote Similarity	NPD6319	Approved
0.68	Remote Similarity	NPD6059	Approved
0.6772	Remote Similarity	NPD6067	Discontinued
0.6759	Remote Similarity	NPD7524	Approved
0.6757	Remote Similarity	NPD6399	Phase 3
0.6746	Remote Similarity	NPD6016	Approved
0.6746	Remote Similarity	NPD6015	Approved
0.6721	Remote Similarity	NPD4632	Approved
0.6696	Remote Similarity	NPD7748	Approved
0.6693	Remote Similarity	NPD5988	Approved
0.6667	Remote Similarity	NPD6411	Approved
0.6667	Remote Similarity	NPD7902	Approved
0.6639	Remote Similarity	NPD7899	Clinical (unspecified phase)
0.6583	Remote Similarity	NPD6881	Approved
0.6583	Remote Similarity	NPD6899	Approved
0.6574	Remote Similarity	NPD1694	Approved
0.6557	Remote Similarity	NPD8130	Phase 1
0.6557	Remote Similarity	NPD6649	Approved
0.6557	Remote Similarity	NPD6650	Approved
0.6555	Remote Similarity	NPD6675	Approved
0.6555	Remote Similarity	NPD5739	Approved
0.6555	Remote Similarity	NPD6402	Approved
0.6555	Remote Similarity	NPD7128	Approved
0.6538	Remote Similarity	NPD8451	Approved
0.6529	Remote Similarity	NPD6372	Approved
0.6529	Remote Similarity	NPD6373	Approved
0.6518	Remote Similarity	NPD7515	Phase 2
0.6512	Remote Similarity	NPD7830	Approved
0.6512	Remote Similarity	NPD7829	Approved
0.6504	Remote Similarity	NPD6053	Discontinued
0.65	Remote Similarity	NPD5697	Approved
0.6489	Remote Similarity	NPD8448	Approved
0.6486	Remote Similarity	NPD6101	Approved
0.6486	Remote Similarity	NPD5764	Clinical (unspecified phase)
0.6484	Remote Similarity	NPD6921	Approved
0.6484	Remote Similarity	NPD8444	Approved
0.6481	Remote Similarity	NPD7338	Clinical (unspecified phase)
0.6475	Remote Similarity	NPD7290	Approved
0.6475	Remote Similarity	NPD7102	Approved
0.6475	Remote Similarity	NPD6371	Approved
0.6475	Remote Similarity	NPD6883	Approved
0.6455	Remote Similarity	NPD4250	Approved
0.6455	Remote Similarity	NPD4251	Approved
0.6446	Remote Similarity	NPD7320	Approved
0.6435	Remote Similarity	NPD7839	Suspended
0.6423	Remote Similarity	NPD6847	Approved
0.6423	Remote Similarity	NPD6617	Approved
0.6423	Remote Similarity	NPD6869	Approved
0.6418	Remote Similarity	NPD7260	Phase 2
0.6417	Remote Similarity	NPD6008	Approved
0.6408	Remote Similarity	NPD8264	Approved
0.6404	Remote Similarity	NPD7901	Clinical (unspecified phase)
0.6404	Remote Similarity	NPD7900	Approved
0.6393	Remote Similarity	NPD6012	Approved
0.6393	Remote Similarity	NPD6014	Approved
0.6393	Remote Similarity	NPD6013	Approved
0.6389	Remote Similarity	NPD6695	Phase 3
0.6385	Remote Similarity	NPD7604	Phase 2
0.6372	Remote Similarity	NPD8035	Phase 2
0.6372	Remote Similarity	NPD8034	Phase 2
0.6364	Remote Similarity	NPD4249	Approved
0.6364	Remote Similarity	NPD7625	Phase 1
0.6364	Remote Similarity	NPD5701	Approved
0.6357	Remote Similarity	NPD5983	Phase 2
0.6343	Remote Similarity	NPD8392	Approved
0.6343	Remote Similarity	NPD8390	Approved
0.6343	Remote Similarity	NPD8391	Approved
0.6339	Remote Similarity	NPD6051	Approved
0.6336	Remote Similarity	NPD8341	Approved
0.6336	Remote Similarity	NPD8340	Approved
0.6336	Remote Similarity	NPD8342	Approved
0.6336	Remote Similarity	NPD8299	Approved
0.6333	Remote Similarity	NPD8170	Clinical (unspecified phase)
0.633	Remote Similarity	NPD4786	Approved
0.6321	Remote Similarity	NPD7645	Phase 2
0.6316	Remote Similarity	NPD8171	Discontinued
0.6316	Remote Similarity	NPD6033	Approved
0.6311	Remote Similarity	NPD6011	Approved
0.6306	Remote Similarity	NPD7750	Discontinued
0.6304	Remote Similarity	NPD7966	Clinical (unspecified phase)
0.6296	Remote Similarity	NPD3667	Approved
0.6296	Remote Similarity	NPD4752	Clinical (unspecified phase)
0.6288	Remote Similarity	NPD6336	Discontinued
0.6283	Remote Similarity	NPD3168	Discontinued
0.6262	Remote Similarity	NPD5790	Clinical (unspecified phase)
0.6262	Remote Similarity	NPD7525	Registered
0.625	Remote Similarity	NPD8039	Approved
0.625	Remote Similarity	NPD8449	Approved
0.6239	Remote Similarity	NPD3670	Clinical (unspecified phase)
0.6239	Remote Similarity	NPD3669	Approved
0.6239	Remote Similarity	NPD6083	Phase 2
0.6239	Remote Similarity	NPD6084	Phase 2
0.6228	Remote Similarity	NPD6079	Approved
0.6218	Remote Similarity	NPD4159	Approved
0.6216	Remote Similarity	NPD3618	Phase 1
0.621	Remote Similarity	NPD4634	Approved
0.6207	Remote Similarity	NPD1698	Clinical (unspecified phase)
0.6204	Remote Similarity	NPD8450	Suspended
0.6195	Remote Similarity	NPD5328	Approved
0.6183	Remote Similarity	NPD5126	Approved
0.6183	Remote Similarity	NPD5125	Phase 3
0.6176	Remote Similarity	NPD7532	Clinical (unspecified phase)
0.6168	Remote Similarity	NPD6929	Approved
0.6167	Remote Similarity	NPD5211	Phase 2
0.6164	Remote Similarity	NPD7799	Discontinued
0.616	Remote Similarity	NPD6401	Clinical (unspecified phase)
0.6134	Remote Similarity	NPD5285	Approved
0.6134	Remote Similarity	NPD5286	Approved
0.6134	Remote Similarity	NPD4696	Approved
0.6131	Remote Similarity	NPD6845	Suspended
0.6126	Remote Similarity	NPD6082	Clinical (unspecified phase)
0.6126	Remote Similarity	NPD7520	Clinical (unspecified phase)
0.6125	Remote Similarity	NPD8470	Clinical (unspecified phase)
0.6124	Remote Similarity	NPD7641	Discontinued
0.6111	Remote Similarity	NPD4819	Approved
0.6111	Remote Similarity	NPD6930	Phase 2
0.6111	Remote Similarity	NPD4822	Approved
0.6111	Remote Similarity	NPD7514	Phase 3
0.6111	Remote Similarity	NPD7332	Phase 2
0.6111	Remote Similarity	NPD4821	Approved
0.6111	Remote Similarity	NPD6931	Approved
0.6111	Remote Similarity	NPD4820	Approved
0.6102	Remote Similarity	NPD4755	Approved
0.6095	Remote Similarity	NPD6942	Approved
0.6095	Remote Similarity	NPD7339	Approved
0.6091	Remote Similarity	NPD7154	Phase 3
0.6077	Remote Similarity	NPD7101	Approved
0.6077	Remote Similarity	NPD7100	Approved
0.6075	Remote Similarity	NPD4271	Approved
0.6075	Remote Similarity	NPD4268	Approved
0.6075	Remote Similarity	NPD7145	Approved
0.6071	Remote Similarity	NPD6409	Approved
0.6071	Remote Similarity	NPD7146	Approved
0.6071	Remote Similarity	NPD6684	Approved
0.6071	Remote Similarity	NPD7521	Approved
0.6071	Remote Similarity	NPD5330	Approved
0.6071	Remote Similarity	NPD7334	Approved
0.6068	Remote Similarity	NPD5695	Phase 3
0.6066	Remote Similarity	NPD5141	Approved
0.6055	Remote Similarity	NPD6902	Approved
0.6047	Remote Similarity	NPD8137	Clinical (unspecified phase)
0.6043	Remote Similarity	NPD8415	Approved
0.6038	Remote Similarity	NPD3701	Clinical (unspecified phase)

Bioactivity similarity: Similar Natural Products in NPASS

Bioactivity similarity was calculated based on bioactivity descriptors of compounds. The bioactivity descriptors were calculated by a recently developed AI algorithm Chemical Checker (CC) [Nature Biotechnology, 38:1087–1096, 2020; Nature Communications, 12:3932, 2021], which evaluated bioactivity similarities at five levels:
☉ A: chemistry similarity;
☉ B: biological targets similarity;
☉ C: networks similarity;
☉ D: cell-based bioactivity similarity;
☉ E: similarity based on clinical data.

Those 5 categories of CC bioactivity descriptors were calculated and then subjected to manifold projection using UMAP algorithm, to project all NPs on a 2-Dimensional space. The current NP was highlighted with a small circle in the 2-D map. Below figures: left-to-right, A-to-E.

A: chemistry similarity

B: biological targets similarity

C: networks similarity

D: cell-based bioactivity similarity

E: similarity based on clinical data