NPASS Compound

Structure

NPC41405 OpenBabel07101718312D 39 43 0 0 1 0 0 0 0 0999 V2000 7.3386 2.1977 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.3386 -0.8023 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.8386 0.0638 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3904 -0.1339 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4394 -0.4429 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7405 -1.3023 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4207 -0.1113 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7405 1.6977 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6720 2.2804 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6666 2.1759 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.4726 -2.3023 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6065 -1.8023 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6180 1.9021 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.4726 0.6977 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0085 -0.3023 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9781 0.2079 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.4726 2.6977 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2872 1.1590 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.2653 1.3669 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.3601 1.6942 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.8745 -0.8023 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.8745 1.1977 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.4726 -0.3023 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 7.3386 -1.8023 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6065 1.1977 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.7405 -0.3023 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.6691 0.7431 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 7.3386 -0.8023 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6473 0.5352 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6065 -0.8023 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.0085 0.6977 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.7405 0.6977 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 6.4726 3.6977 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.0292 2.4373 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.8745 -1.8023 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 8.2046 -2.3023 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.3164 1.2784 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 5.6065 2.1977 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 17 1 0 0 0 0 2 28 1 0 0 0 0 3 28 1 0 0 0 0 4 29 1 0 0 0 0 5 29 1 0 0 0 0 9 10 1 0 0 0 0 9 19 1 0 0 0 0 10 22 2 0 0 0 0 11 12 2 0 0 0 0 11 24 1 0 0 0 0 12 30 1 0 0 0 0 13 20 1 0 0 0 0 14 23 1 0 0 0 0 14 25 1 0 0 0 0 15 21 1 0 0 0 0 15 31 1 0 0 0 0 16 18 1 0 0 0 0 16 38 1 0 0 0 0 17 33 2 0 0 0 0 17 39 1 0 0 0 0 18 13 1 1 0 0 0 18 19 1 0 0 0 0 19 31 1 6 0 0 0 20 27 1 0 0 0 0 20 34 1 6 0 0 0 21 26 1 0 0 0 0 21 35 1 6 0 0 0 22 31 1 0 0 0 0 22 32 1 0 0 0 0 23 28 1 0 0 0 0 23 30 1 1 0 0 0 24 28 1 0 0 0 0 24 36 2 0 0 0 0 25 32 1 6 0 0 0 25 39 1 0 0 0 0 26 30 1 1 0 0 0 26 32 1 0 0 0 0 27 29 1 1 0 0 0 27 38 1 0 0 0 0 29 37 1 0 0 0 0 30 6 1 1 0 0 0 31 7 1 6 0 0 0 32 8 1 1 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	544.34
Volume:	570.231
LogP:	3.329
LogD:	2.793
LogS:	-4.246
# Rotatable Bonds:	4
TPSA:	113.29
# H-Bond Aceptor:	7
# H-Bond Donor:	3
# Rings:	5
# Heavy Atoms:	7

MedChem Properties

QED Drug-Likeness Score:	0.364
Synthetic Accessibility Score:	5.588
Fsp3:	0.812
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:	-5.162
MDCK Permeability:	7.617410119564738e-06
Pgp-inhibitor:	0.997
Pgp-substrate:	0.179
Human Intestinal Absorption (HIA):	0.005
20% Bioavailability (F20%):	0.024
30% Bioavailability (F30%):	0.208

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.075
Plasma Protein Binding (PPB):	79.27556610107422%
Volume Distribution (VD):	1.218
Pgp-substrate:	15.370438575744629%

ADMET: Metabolism

CYP1A2-inhibitor:	0.003
CYP1A2-substrate:	0.122
CYP2C19-inhibitor:	0.011
CYP2C19-substrate:	0.576
CYP2C9-inhibitor:	0.051
CYP2C9-substrate:	0.043
CYP2D6-inhibitor:	0.006
CYP2D6-substrate:	0.025
CYP3A4-inhibitor:	0.756
CYP3A4-substrate:	0.567

ADMET: Excretion

Clearance (CL):	1.875
Half-life (T1/2):	0.409

ADMET: Toxicity

hERG Blockers:	0.245
Human Hepatotoxicity (H-HT):	0.427
Drug-inuced Liver Injury (DILI):	0.211
AMES Toxicity:	0.023
Rat Oral Acute Toxicity:	0.711
Maximum Recommended Daily Dose:	0.91
Skin Sensitization:	0.928
Carcinogencity:	0.076
Eye Corrosion:	0.004
Eye Irritation:	0.013
Respiratory Toxicity:	0.971

Download Data

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

Natural Product: NPC41405

Natural Product ID:	NPC41405
*Common Name:**	Toonaciliatavarin B
IUPAC Name:	[(5R,7R,8R,9R,10S,11R,13S,17S)-11-hydroxy-17-[(3S,5R,6R)-5-hydroxy-6-(2-hydroxypropan-2-yl)oxan-3-yl]-4,4,8,10,13-pentamethyl-3-oxo-5,6,7,9,11,12,16,17-octahydrocyclopenta[a]phenanthren-7-yl] acetate
Synonyms:	Toonaciliatavarin B
Standard InCHIKey:	SYXDKQWRJLIHHO-QGJRNOJXSA-N
Standard InCHI:	InChI=1S/C32H48O7/c1-17(33)39-25-14-23-28(2,3)24(36)11-12-30(23,6)26-21(35)15-31(7)19(9-10-22(31)32(25,26)8)18-13-20(34)27(38-16-18)29(4,5)37/h10-12,18-21,23,25-27,34-35,37H,9,13-16H2,1-8H3/t18-,19+,20-,21-,23+,25-,26-,27-,30+,31+,32-/m1/s1
SMILES:	CC(=O)O[C@@H]1C[C@H]2C(C)(C)C(=O)C=C[C@]2(C)[C@H]2[C@@H](C[C@@]3(C)[C@@H](CC=C3[C@]12C)[C@@H]1C[C@H]([C@H](C(C)(C)O)OC1)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL2035082
PubChem CID:	57409758
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001553] Triterpenoids

*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
NPO13083	Toona ciliata	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19275174]
NPO13083	Toona ciliata	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[22537362]
NPO13083	Toona ciliata	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[31503490]
NPO13083	Toona ciliata	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO13083	Toona ciliata	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO13083	Toona ciliata	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO13083	Toona ciliata	Species	Meliaceae	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	7

Activity Type	# Activity
Cell Line	5
NON-MOLECULAR	1
Others	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT83	Cell Line	MCF7	Homo sapiens	IC50	>	50000.0	nM	PMID[572230]
NPT91	Cell Line	KB	Homo sapiens	IC50	>	50000.0	nM	PMID[572230]
NPT659	Cell Line	SMMC-7721	Homo sapiens	IC50	>	50000.0	nM	PMID[572230]
NPT111	Cell Line	K562	Homo sapiens	IC50	>	50000.0	nM	PMID[572230]
NPT113	Cell Line	RAW264.7	Mus musculus	IC50	=	7900.0	nM	PMID[572230]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	IC50	>	50000.0	nM	PMID[572230]
NPT2	Others	Unspecified		IC50	>	50000	nM	PMID[20086162]

☑ 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 NPC41405 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	225
0.1-0.2	1331
0.2-0.3	4225
0.3-0.4	8635
0.4-0.5	12493
0.5-0.6	6688
0.6-0.7	5498
0.7-0.8	3268
0.8-0.85	298
0.85-0.9	33
0.9-0.95	1
0.95-1	2

Similarity Score	Similarity Level	Natural Product ID
0.9615	High Similarity	NPC255017
0.9333	High Similarity	NPC234042
0.9333	High Similarity	NPC152117
0.9327	High Similarity	NPC5284
0.9118	High Similarity	NPC264048
0.8932	High Similarity	NPC239716
0.8835	High Similarity	NPC473163
0.8785	High Similarity	NPC239097
0.8738	High Similarity	NPC469327
0.8727	High Similarity	NPC270929
0.87	High Similarity	NPC240617
0.8661	High Similarity	NPC161065
0.8661	High Similarity	NPC61520
0.8649	High Similarity	NPC470959
0.8649	High Similarity	NPC476965
0.8614	High Similarity	NPC473170
0.8614	High Similarity	NPC473415
0.8614	High Similarity	NPC37787
0.8614	High Similarity	NPC30677
0.8614	High Similarity	NPC469329
0.8614	High Similarity	NPC180557
0.8611	High Similarity	NPC197428
0.86	High Similarity	NPC79117
0.8598	High Similarity	NPC469844
0.8584	High Similarity	NPC241192
0.8571	High Similarity	NPC329736
0.8545	High Similarity	NPC194100
0.8529	High Similarity	NPC471822
0.8505	High Similarity	NPC44063
0.8505	High Similarity	NPC9457
0.8505	High Similarity	NPC471783
0.8491	Intermediate Similarity	NPC75531
0.8491	Intermediate Similarity	NPC149124
0.8482	Intermediate Similarity	NPC471854
0.8482	Intermediate Similarity	NPC470493
0.8482	Intermediate Similarity	NPC183580
0.8482	Intermediate Similarity	NPC312824
0.8476	Intermediate Similarity	NPC473928
0.8447	Intermediate Similarity	NPC473456
0.8447	Intermediate Similarity	NPC292133
0.8426	Intermediate Similarity	NPC293850
0.8421	Intermediate Similarity	NPC476961
0.8407	Intermediate Similarity	NPC709
0.8407	Intermediate Similarity	NPC50774
0.8407	Intermediate Similarity	NPC257457
0.8407	Intermediate Similarity	NPC311554
0.8396	Intermediate Similarity	NPC324001
0.8393	Intermediate Similarity	NPC251236
0.8393	Intermediate Similarity	NPC302471
0.8393	Intermediate Similarity	NPC134869
0.8393	Intermediate Similarity	NPC235539
0.8393	Intermediate Similarity	NPC176840
0.8393	Intermediate Similarity	NPC96312
0.8393	Intermediate Similarity	NPC40632
0.8393	Intermediate Similarity	NPC152199
0.8393	Intermediate Similarity	NPC328374
0.8378	Intermediate Similarity	NPC49451
0.8365	Intermediate Similarity	NPC114274
0.8365	Intermediate Similarity	NPC470068
0.8364	Intermediate Similarity	NPC201992
0.8362	Intermediate Similarity	NPC473979
0.8362	Intermediate Similarity	NPC469789
0.835	Intermediate Similarity	NPC471777
0.8349	Intermediate Similarity	NPC173905
0.8349	Intermediate Similarity	NPC2766
0.8349	Intermediate Similarity	NPC218853
0.8349	Intermediate Similarity	NPC472216
0.8349	Intermediate Similarity	NPC5475
0.8349	Intermediate Similarity	NPC284828
0.8348	Intermediate Similarity	NPC202051
0.8333	Intermediate Similarity	NPC475294
0.8333	Intermediate Similarity	NPC144459
0.8333	Intermediate Similarity	NPC473203
0.8319	Intermediate Similarity	NPC284068
0.8319	Intermediate Similarity	NPC140055
0.8319	Intermediate Similarity	NPC167606
0.8319	Intermediate Similarity	NPC286528
0.8319	Intermediate Similarity	NPC20302
0.8318	Intermediate Similarity	NPC255309
0.8318	Intermediate Similarity	NPC471293
0.8317	Intermediate Similarity	NPC473166
0.8304	Intermediate Similarity	NPC67259
0.8304	Intermediate Similarity	NPC147912
0.8304	Intermediate Similarity	NPC18547
0.8304	Intermediate Similarity	NPC473798
0.8304	Intermediate Similarity	NPC474906
0.8304	Intermediate Similarity	NPC243354
0.8302	Intermediate Similarity	NPC136289
0.8291	Intermediate Similarity	NPC473255
0.8288	Intermediate Similarity	NPC71348
0.8288	Intermediate Similarity	NPC289312
0.8288	Intermediate Similarity	NPC470063
0.8288	Intermediate Similarity	NPC90769
0.8288	Intermediate Similarity	NPC11252
0.8286	Intermediate Similarity	NPC316964
0.8286	Intermediate Similarity	NPC167974
0.8273	Intermediate Similarity	NPC250956
0.8273	Intermediate Similarity	NPC473627
0.8273	Intermediate Similarity	NPC37116
0.8273	Intermediate Similarity	NPC29133
0.8269	Intermediate Similarity	NPC108078
0.8261	Intermediate Similarity	NPC474370
0.8261	Intermediate Similarity	NPC79579
0.8257	Intermediate Similarity	NPC472218
0.8257	Intermediate Similarity	NPC472219
0.8257	Intermediate Similarity	NPC472217
0.8252	Intermediate Similarity	NPC317586
0.8252	Intermediate Similarity	NPC470016
0.8246	Intermediate Similarity	NPC153440
0.8246	Intermediate Similarity	NPC297179
0.8246	Intermediate Similarity	NPC186525
0.8241	Intermediate Similarity	NPC231530
0.8241	Intermediate Similarity	NPC470587
0.8241	Intermediate Similarity	NPC181265
0.8241	Intermediate Similarity	NPC96377
0.8241	Intermediate Similarity	NPC102352
0.8241	Intermediate Similarity	NPC278628
0.8235	Intermediate Similarity	NPC477436
0.8235	Intermediate Similarity	NPC469315
0.8235	Intermediate Similarity	NPC477435
0.823	Intermediate Similarity	NPC64318
0.823	Intermediate Similarity	NPC190286
0.823	Intermediate Similarity	NPC243981
0.822	Intermediate Similarity	NPC473635
0.822	Intermediate Similarity	NPC293112
0.8214	Intermediate Similarity	NPC250109
0.8214	Intermediate Similarity	NPC194273
0.8214	Intermediate Similarity	NPC25909
0.8214	Intermediate Similarity	NPC208998
0.8214	Intermediate Similarity	NPC51978
0.8214	Intermediate Similarity	NPC7921
0.8208	Intermediate Similarity	NPC81530
0.8208	Intermediate Similarity	NPC233012
0.8208	Intermediate Similarity	NPC470054
0.8208	Intermediate Similarity	NPC54909
0.8208	Intermediate Similarity	NPC476223
0.8208	Intermediate Similarity	NPC476240
0.8208	Intermediate Similarity	NPC224720
0.8205	Intermediate Similarity	NPC11895
0.8198	Intermediate Similarity	NPC146945
0.8198	Intermediate Similarity	NPC171888
0.8198	Intermediate Similarity	NPC471243
0.8198	Intermediate Similarity	NPC474229
0.8198	Intermediate Similarity	NPC470961
0.819	Intermediate Similarity	NPC46570
0.819	Intermediate Similarity	NPC194196
0.819	Intermediate Similarity	NPC67569
0.819	Intermediate Similarity	NPC471582
0.8182	Intermediate Similarity	NPC246205
0.8182	Intermediate Similarity	NPC27814
0.8182	Intermediate Similarity	NPC475065
0.8182	Intermediate Similarity	NPC471855
0.8182	Intermediate Similarity	NPC310546
0.8174	Intermediate Similarity	NPC475041
0.8174	Intermediate Similarity	NPC470777
0.8174	Intermediate Similarity	NPC5292
0.8174	Intermediate Similarity	NPC476529
0.8174	Intermediate Similarity	NPC473636
0.8174	Intermediate Similarity	NPC469488
0.8174	Intermediate Similarity	NPC77689
0.8174	Intermediate Similarity	NPC475775
0.8174	Intermediate Similarity	NPC264954
0.8174	Intermediate Similarity	NPC476960
0.8173	Intermediate Similarity	NPC471039
0.8165	Intermediate Similarity	NPC59530
0.8165	Intermediate Similarity	NPC3316
0.8165	Intermediate Similarity	NPC473284
0.8165	Intermediate Similarity	NPC144854
0.8158	Intermediate Similarity	NPC470492
0.8158	Intermediate Similarity	NPC97908
0.8158	Intermediate Similarity	NPC122033
0.8158	Intermediate Similarity	NPC474654
0.8158	Intermediate Similarity	NPC473968
0.8158	Intermediate Similarity	NPC470854
0.8158	Intermediate Similarity	NPC287343
0.8155	Intermediate Similarity	NPC166906
0.8155	Intermediate Similarity	NPC473172
0.8155	Intermediate Similarity	NPC159410
0.8151	Intermediate Similarity	NPC470882
0.8151	Intermediate Similarity	NPC473265
0.8151	Intermediate Similarity	NPC473253
0.8148	Intermediate Similarity	NPC235889
0.8148	Intermediate Similarity	NPC137657
0.8148	Intermediate Similarity	NPC65523
0.8148	Intermediate Similarity	NPC473175
0.8142	Intermediate Similarity	NPC165439
0.8142	Intermediate Similarity	NPC74727
0.8142	Intermediate Similarity	NPC473882
0.8142	Intermediate Similarity	NPC471398
0.8142	Intermediate Similarity	NPC470953
0.8137	Intermediate Similarity	NPC218301
0.8136	Intermediate Similarity	NPC8369
0.8131	Intermediate Similarity	NPC22388
0.8131	Intermediate Similarity	NPC469316
0.8131	Intermediate Similarity	NPC470053
0.8125	Intermediate Similarity	NPC475524
0.8125	Intermediate Similarity	NPC269530
0.8125	Intermediate Similarity	NPC474516
0.8125	Intermediate Similarity	NPC280782
0.8125	Intermediate Similarity	NPC100267

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 NPC41405 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	195
0.1-0.2	1606
0.2-0.3	3686
0.3-0.4	2359
0.4-0.5	785
0.5-0.6	249
0.6-0.7	139
0.7-0.8	121
0.8-0.85	10
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8796	High Similarity	NPD8297	Approved
0.8598	High Similarity	NPD6881	Approved
0.8598	High Similarity	NPD6899	Approved
0.8532	High Similarity	NPD8130	Phase 1
0.8505	High Similarity	NPD5697	Approved
0.844	Intermediate Similarity	NPD7102	Approved
0.844	Intermediate Similarity	NPD7290	Approved
0.844	Intermediate Similarity	NPD6883	Approved
0.8411	Intermediate Similarity	NPD5739	Approved
0.8411	Intermediate Similarity	NPD7128	Approved
0.8411	Intermediate Similarity	NPD6675	Approved
0.8411	Intermediate Similarity	NPD6402	Approved
0.8364	Intermediate Similarity	NPD6650	Approved
0.8364	Intermediate Similarity	NPD6869	Approved
0.8364	Intermediate Similarity	NPD6649	Approved
0.8364	Intermediate Similarity	NPD6847	Approved
0.8364	Intermediate Similarity	NPD6617	Approved
0.8349	Intermediate Similarity	NPD6012	Approved
0.8349	Intermediate Similarity	NPD6013	Approved
0.8349	Intermediate Similarity	NPD6014	Approved
0.8319	Intermediate Similarity	NPD7115	Discovery
0.8288	Intermediate Similarity	NPD6882	Approved
0.8257	Intermediate Similarity	NPD7320	Approved
0.8257	Intermediate Similarity	NPD6011	Approved
0.8214	Intermediate Similarity	NPD4632	Approved
0.8182	Intermediate Similarity	NPD6373	Approved
0.8182	Intermediate Similarity	NPD6372	Approved
0.8165	Intermediate Similarity	NPD5701	Approved
0.8137	Intermediate Similarity	NPD6079	Approved
0.8113	Intermediate Similarity	NPD5286	Approved
0.8113	Intermediate Similarity	NPD5285	Approved
0.8113	Intermediate Similarity	NPD4696	Approved
0.8103	Intermediate Similarity	NPD6319	Approved
0.7981	Intermediate Similarity	NPD7748	Approved
0.7963	Intermediate Similarity	NPD5224	Approved
0.7963	Intermediate Similarity	NPD5226	Approved
0.7963	Intermediate Similarity	NPD5225	Approved
0.7963	Intermediate Similarity	NPD5211	Phase 2
0.7963	Intermediate Similarity	NPD4633	Approved
0.7941	Intermediate Similarity	NPD5328	Approved
0.7934	Intermediate Similarity	NPD7736	Approved
0.7925	Intermediate Similarity	NPD7902	Approved
0.7925	Intermediate Similarity	NPD4755	Approved
0.7921	Intermediate Similarity	NPD3573	Approved
0.789	Intermediate Similarity	NPD5175	Approved
0.789	Intermediate Similarity	NPD5174	Approved
0.7885	Intermediate Similarity	NPD6399	Phase 3
0.7876	Intermediate Similarity	NPD6401	Clinical (unspecified phase)
0.787	Intermediate Similarity	NPD5223	Approved
0.7863	Intermediate Similarity	NPD7101	Approved
0.7863	Intermediate Similarity	NPD7100	Approved
0.7845	Intermediate Similarity	NPD6009	Approved
0.7833	Intermediate Similarity	NPD7492	Approved
0.783	Intermediate Similarity	NPD5220	Clinical (unspecified phase)
0.783	Intermediate Similarity	NPD5221	Approved
0.783	Intermediate Similarity	NPD5222	Approved
0.7818	Intermediate Similarity	NPD5141	Approved
0.7797	Intermediate Similarity	NPD6054	Approved
0.7788	Intermediate Similarity	NPD7515	Phase 2
0.7788	Intermediate Similarity	NPD4634	Approved
0.7778	Intermediate Similarity	NPD6335	Approved
0.7778	Intermediate Similarity	NPD4700	Approved
0.7769	Intermediate Similarity	NPD6616	Approved
0.7759	Intermediate Similarity	NPD6274	Approved
0.7757	Intermediate Similarity	NPD6084	Phase 2
0.7757	Intermediate Similarity	NPD5173	Approved
0.7757	Intermediate Similarity	NPD6083	Phase 2
0.775	Intermediate Similarity	NPD7604	Phase 2
0.7731	Intermediate Similarity	NPD5983	Phase 2
0.7705	Intermediate Similarity	NPD7078	Approved
0.7692	Intermediate Similarity	NPD6317	Approved
0.7679	Intermediate Similarity	NPD6412	Phase 2
0.7667	Intermediate Similarity	NPD6370	Approved
0.7642	Intermediate Similarity	NPD7901	Clinical (unspecified phase)
0.7642	Intermediate Similarity	NPD7900	Approved
0.7627	Intermediate Similarity	NPD6313	Approved
0.7627	Intermediate Similarity	NPD6314	Approved
0.7623	Intermediate Similarity	NPD7507	Approved
0.7623	Intermediate Similarity	NPD6336	Discontinued
0.7611	Intermediate Similarity	NPD4730	Approved
0.7611	Intermediate Similarity	NPD4729	Approved
0.7607	Intermediate Similarity	NPD6868	Approved
0.7603	Intermediate Similarity	NPD8328	Phase 3
0.7589	Intermediate Similarity	NPD6008	Approved
0.7583	Intermediate Similarity	NPD6015	Approved
0.7583	Intermediate Similarity	NPD6016	Approved
0.7561	Intermediate Similarity	NPD8293	Discontinued
0.7547	Intermediate Similarity	NPD4202	Approved
0.7544	Intermediate Similarity	NPD8132	Clinical (unspecified phase)
0.7521	Intermediate Similarity	NPD5988	Approved
0.75	Intermediate Similarity	NPD6059	Approved
0.75	Intermediate Similarity	NPD4697	Phase 3
0.7478	Intermediate Similarity	NPD5249	Phase 3
0.7478	Intermediate Similarity	NPD5248	Approved
0.7478	Intermediate Similarity	NPD5250	Approved
0.7478	Intermediate Similarity	NPD5251	Approved
0.7478	Intermediate Similarity	NPD5247	Approved
0.7476	Intermediate Similarity	NPD3618	Phase 1
0.7456	Intermediate Similarity	NPD5128	Approved
0.7456	Intermediate Similarity	NPD5345	Clinical (unspecified phase)
0.7453	Intermediate Similarity	NPD8035	Phase 2
0.7453	Intermediate Similarity	NPD8034	Phase 2
0.7453	Intermediate Similarity	NPD6411	Approved
0.7451	Intermediate Similarity	NPD4786	Approved
0.744	Intermediate Similarity	NPD7319	Approved
0.7438	Intermediate Similarity	NPD6291	Clinical (unspecified phase)
0.7438	Intermediate Similarity	NPD6909	Approved
0.7438	Intermediate Similarity	NPD6908	Approved
0.7434	Intermediate Similarity	NPD4768	Approved
0.7434	Intermediate Similarity	NPD4767	Approved
0.7414	Intermediate Similarity	NPD5217	Approved
0.7414	Intermediate Similarity	NPD5215	Approved
0.7414	Intermediate Similarity	NPD5216	Approved
0.7411	Intermediate Similarity	NPD4754	Approved
0.7407	Intermediate Similarity	NPD5695	Phase 3
0.7395	Intermediate Similarity	NPD8295	Clinical (unspecified phase)
0.7391	Intermediate Similarity	NPD4061	Clinical (unspecified phase)
0.7364	Intermediate Similarity	NPD5696	Approved
0.7364	Intermediate Similarity	NPD4225	Approved
0.7333	Intermediate Similarity	NPD5737	Approved
0.7333	Intermediate Similarity	NPD7513	Clinical (unspecified phase)
0.7333	Intermediate Similarity	NPD6672	Approved
0.7328	Intermediate Similarity	NPD5169	Approved
0.7328	Intermediate Similarity	NPD5135	Approved
0.7328	Intermediate Similarity	NPD5134	Clinical (unspecified phase)
0.7308	Intermediate Similarity	NPD5330	Approved
0.7308	Intermediate Similarity	NPD7521	Approved
0.7308	Intermediate Similarity	NPD7334	Approved
0.7308	Intermediate Similarity	NPD6409	Approved
0.7308	Intermediate Similarity	NPD6684	Approved
0.7308	Intermediate Similarity	NPD7146	Approved
0.7304	Intermediate Similarity	NPD6686	Approved
0.7265	Intermediate Similarity	NPD5127	Approved
0.7264	Intermediate Similarity	NPD4753	Phase 2
0.7264	Intermediate Similarity	NPD5764	Clinical (unspecified phase)
0.7264	Intermediate Similarity	NPD6101	Approved
0.7255	Intermediate Similarity	NPD3667	Approved
0.7248	Intermediate Similarity	NPD5210	Approved
0.7248	Intermediate Similarity	NPD4629	Approved
0.7248	Intermediate Similarity	NPD6356	Clinical (unspecified phase)
0.7212	Intermediate Similarity	NPD7520	Clinical (unspecified phase)
0.7207	Intermediate Similarity	NPD7638	Approved
0.717	Intermediate Similarity	NPD6903	Approved
0.7155	Intermediate Similarity	NPD5168	Approved
0.7154	Intermediate Similarity	NPD7503	Approved
0.7154	Intermediate Similarity	NPD8033	Approved
0.7143	Intermediate Similarity	NPD7640	Approved
0.7143	Intermediate Similarity	NPD7639	Approved
0.7143	Intermediate Similarity	NPD3574	Clinical (unspecified phase)
0.713	Intermediate Similarity	NPD5284	Approved
0.713	Intermediate Similarity	NPD5281	Approved
0.7115	Intermediate Similarity	NPD3133	Approved
0.7115	Intermediate Similarity	NPD3665	Phase 1
0.7115	Intermediate Similarity	NPD3666	Approved
0.7103	Intermediate Similarity	NPD6904	Approved
0.7103	Intermediate Similarity	NPD6673	Approved
0.7103	Intermediate Similarity	NPD6080	Approved
0.7083	Intermediate Similarity	NPD5167	Approved
0.7073	Intermediate Similarity	NPD8294	Approved
0.7073	Intermediate Similarity	NPD8377	Approved
0.7049	Intermediate Similarity	NPD7327	Approved
0.7049	Intermediate Similarity	NPD7328	Approved
0.7034	Intermediate Similarity	NPD5955	Clinical (unspecified phase)
0.7016	Intermediate Similarity	NPD8296	Approved
0.7016	Intermediate Similarity	NPD8378	Approved
0.7016	Intermediate Similarity	NPD8380	Approved
0.7016	Intermediate Similarity	NPD8335	Approved
0.7016	Intermediate Similarity	NPD8379	Approved
0.7	Intermediate Similarity	NPD8133	Approved
0.6992	Remote Similarity	NPD7516	Approved
0.6953	Remote Similarity	NPD6033	Approved
0.6944	Remote Similarity	NPD7285	Clinical (unspecified phase)
0.6937	Remote Similarity	NPD1698	Clinical (unspecified phase)
0.6923	Remote Similarity	NPD4223	Phase 3
0.6923	Remote Similarity	NPD4221	Approved
0.6917	Remote Similarity	NPD6053	Discontinued
0.6893	Remote Similarity	NPD7525	Registered
0.6887	Remote Similarity	NPD5329	Approved
0.6887	Remote Similarity	NPD1694	Approved
0.688	Remote Similarity	NPD8517	Approved
0.688	Remote Similarity	NPD8516	Approved
0.688	Remote Similarity	NPD8515	Approved
0.688	Remote Similarity	NPD8513	Phase 3
0.6852	Remote Similarity	NPD5208	Approved
0.6847	Remote Similarity	NPD6001	Approved
0.6822	Remote Similarity	NPD5690	Phase 2
0.6822	Remote Similarity	NPD5279	Phase 3
0.6822	Remote Similarity	NPD6098	Approved
0.6818	Remote Similarity	NPD5694	Approved
0.6818	Remote Similarity	NPD5693	Phase 1
0.6818	Remote Similarity	NPD6050	Approved
0.6792	Remote Similarity	NPD3668	Phase 3
0.6792	Remote Similarity	NPD4197	Approved
0.678	Remote Similarity	NPD5954	Clinical (unspecified phase)
0.6765	Remote Similarity	NPD6116	Phase 1
0.6762	Remote Similarity	NPD6435	Approved
0.6757	Remote Similarity	NPD5779	Approved
0.6757	Remote Similarity	NPD5778	Approved
0.675	Remote Similarity	NPD6371	Approved
0.6746	Remote Similarity	NPD6921	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