NPASS Compound

Structure

CID322420 OpenBabel06191716162D 43 50 0 0 1 0 0 0 0 0999 V2000 2.0777 1.8345 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9410 1.1506 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7031 -4.0719 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6768 -1.4546 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3179 -1.9509 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.6915 -2.2092 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9937 1.7935 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.8567 -1.4774 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9752 -2.4321 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3661 2.2046 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9514 1.0445 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.3055 -0.9685 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.4240 -1.9232 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6963 1.8667 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2816 0.7066 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4614 -2.3167 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4408 1.1781 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1745 -3.4326 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2931 -0.5471 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 6.5891 -1.1914 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6541 1.1177 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5112 -1.6991 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.4447 0.1552 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.9754 -3.5045 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8245 -0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.5633 -0.1209 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.2931 1.2973 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 6.0379 -0.6824 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5267 -2.1966 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.0448 -1.1675 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.3991 -2.4332 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.8245 0.7502 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.5314 -0.5471 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.0000 0.7502 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 1.4201 -4.2048 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.2031 0.0494 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.0324 -2.8542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.1270 -2.0351 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.6053 -1.1282 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.7105 -0.2272 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.5314 1.2973 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.9124 0.1170 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 17 2 0 0 0 0 2 17 1 0 0 0 0 3 18 1 0 0 0 0 4 19 1 0 0 0 0 6 8 2 0 0 0 0 6 9 1 0 0 0 0 7 10 2 0 0 0 0 7 11 1 0 0 0 0 8 12 1 0 0 0 0 9 13 2 0 0 0 0 10 14 1 0 0 0 0 11 15 2 0 0 0 0 12 20 2 0 0 0 0 13 20 1 0 0 0 0 14 21 2 0 0 0 0 15 21 1 0 0 0 0 16 18 2 0 0 0 0 16 22 1 0 0 0 0 18 24 1 0 0 0 0 19 25 1 0 0 0 0 19 33 1 1 0 0 0 20 28 1 0 0 0 0 21 34 1 0 0 0 0 22 31 1 1 0 0 0 22 33 1 0 0 0 0 23 26 1 0 0 0 0 23 27 1 0 0 0 0 23 33 1 6 0 0 0 24 31 1 0 0 0 0 24 35 2 0 0 0 0 25 32 1 1 0 0 0 25 39 1 0 0 0 0 26 30 1 6 0 0 0 26 40 1 0 0 0 0 27 32 1 1 0 0 0 27 41 1 0 0 0 0 28 36 2 0 0 0 0 28 39 1 0 0 0 0 29 30 1 1 0 0 0 29 31 1 0 0 0 0 29 37 1 0 0 0 0 30 5 1 1 0 0 0 30 40 1 0 0 0 0 31 38 1 1 0 0 0 32 17 1 1 0 0 0 32 42 1 0 0 0 0 33 43 1 1 0 0 0 34 41 1 0 0 0 0 34 42 1 0 0 0 0 34 43 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	586.22
Volume:	580.916
LogP:	4.525
LogD:	3.497
LogS:	-4.347
# Rotatable Bonds:	5
TPSA:	124.05
# H-Bond Aceptor:	9
# H-Bond Donor:	2
# Rings:	8
# Heavy Atoms:	9

MedChem Properties

QED Drug-Likeness Score:	0.316
Synthetic Accessibility Score:	6.365
Fsp3:	0.471
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:	-5.154
MDCK Permeability:	3.8313984987325966e-05
Pgp-inhibitor:	0.997
Pgp-substrate:	0.001
Human Intestinal Absorption (HIA):	0.008
20% Bioavailability (F20%):	0.038
30% Bioavailability (F30%):	0.982

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.879
Plasma Protein Binding (PPB):	87.45838165283203%
Volume Distribution (VD):	2.526
Pgp-substrate:	7.530836582183838%

ADMET: Metabolism

CYP1A2-inhibitor:	0.037
CYP1A2-substrate:	0.968
CYP2C19-inhibitor:	0.088
CYP2C19-substrate:	0.445
CYP2C9-inhibitor:	0.497
CYP2C9-substrate:	0.007
CYP2D6-inhibitor:	0.006
CYP2D6-substrate:	0.157
CYP3A4-inhibitor:	0.452
CYP3A4-substrate:	0.566

ADMET: Excretion

Clearance (CL):	6.884
Half-life (T1/2):	0.187

ADMET: Toxicity

hERG Blockers:	0.599
Human Hepatotoxicity (H-HT):	0.913
Drug-inuced Liver Injury (DILI):	0.952
AMES Toxicity:	0.195
Rat Oral Acute Toxicity:	0.737
Maximum Recommended Daily Dose:	0.952
Skin Sensitization:	0.362
Carcinogencity:	0.611
Eye Corrosion:	0.004
Eye Irritation:	0.016
Respiratory Toxicity:	0.986

Download Data

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

Natural Product: NPC322420

Natural Product ID:	NPC322420
*Common Name:**	Trigoxyphin A
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	XVFFINDRMYVYJL-PULFBTHPSA-N
Standard InCHI:	InChI=1S/C34H34O9/c1-17(2)32-25(39-28(36)20-12-8-6-9-13-20)19(4)33-22-16-18(3)24(35)31(22,38)29(37)30(5)26(40-30)23(33)27(32)41-34(42-32,43-33)21-14-10-7-11-15-21/h6-16,19,22-23,25-27,29,37-38H,1H2,2-5H3/t19-,22-,23+,25+,26+,27-,29-,30+,31-,32+,33+,34?/m1/s1
SMILES:	C=C(C)[C@]12[C@H]([C@@H](C)[C@]34[C@@H]5C=C(C)C(=O)[C@]5([C@@H]([C@]5(C)[C@H]([C@H]3[C@H]1OC(c1ccccc1)(O2)O4)O5)O)O)OC(=O)c1ccccc1
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL1172562
PubChem CID:	46872584
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001551] Diterpenoids [CHEMONTID:0003494] Rhamnofolane and daphnane 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
NPO10718	Trigonostemon xyphophylloides	Species	Euphorbiaceae	Eukaryota	Stems	n.a.	n.a.	PMID[20593838]
NPO31570	Trigonostemon thyrsoideum	Species	Euphorbiaceae	Eukaryota	n.a.	root	n.a.	PMID[21192108]
NPO19424	Trigonostemon howii	Species	Euphorbiaceae	Eukaryota	n.a.	twig	n.a.	PMID[21520897]
NPO19424	Trigonostemon howii	Species	Euphorbiaceae	Eukaryota	Stems	n.a.	n.a.	PMID[23148674]
NPO19424	Trigonostemon howii	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23215460]
NPO10718	Trigonostemon xyphophylloides	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19424	Trigonostemon howii	Species	Euphorbiaceae	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	6

Activity Type	# Activity
Cell Line	6

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT116	Cell Line	HL-60	Homo sapiens	IC50	=	270.0	nM	PMID[468077]
NPT81	Cell Line	A549	Homo sapiens	IC50	=	7500.0	nM	PMID[468077]
NPT181	Cell Line	Bel-7402	Homo sapiens	IC50	>	10000.0	nM	PMID[468077]
NPT116	Cell Line	HL-60	Homo sapiens	IC50	>	10000.0	nM	PMID[468078]
NPT81	Cell Line	A549	Homo sapiens	IC50	>	10000.0	nM	PMID[468078]
NPT83	Cell Line	MCF7	Homo sapiens	IC50	>	10000.0	nM	PMID[468078]

☑ 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 NPC322420 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	358
0.1-0.2	1246
0.2-0.3	2693
0.3-0.4	5384
0.4-0.5	10487
0.5-0.6	11247
0.6-0.7	9423
0.7-0.8	1509
0.8-0.85	202
0.85-0.9	117
0.9-0.95	9
0.95-1	22

Similarity Score	Similarity Level	Natural Product ID
0.974	High Similarity	NPC324769
0.974	High Similarity	NPC325732
0.9673	High Similarity	NPC43304
0.9673	High Similarity	NPC477190
0.9673	High Similarity	NPC477188
0.9613	High Similarity	NPC61891
0.9484	High Similarity	NPC66193
0.9477	High Similarity	NPC49297
0.9419	High Similarity	NPC275477
0.9412	High Similarity	NPC181924
0.9367	High Similarity	NPC40138
0.9216	High Similarity	NPC146310
0.9177	High Similarity	NPC471134
0.9156	High Similarity	NPC251139
0.8974	High Similarity	NPC154675
0.8875	High Similarity	NPC478073
0.8854	High Similarity	NPC290683
0.8854	High Similarity	NPC475548
0.8854	High Similarity	NPC475638
0.8805	High Similarity	NPC326328
0.8805	High Similarity	NPC323356
0.8805	High Similarity	NPC471138
0.8805	High Similarity	NPC309991
0.8734	High Similarity	NPC11410
0.8726	High Similarity	NPC471135
0.8718	High Similarity	NPC472398
0.8701	High Similarity	NPC477737
0.8698	High Similarity	NPC254588
0.8679	High Similarity	NPC318447
0.8679	High Similarity	NPC322048
0.8671	High Similarity	NPC5115
0.8671	High Similarity	NPC472549
0.8616	High Similarity	NPC106895
0.8616	High Similarity	NPC323001
0.8616	High Similarity	NPC326235
0.8599	High Similarity	NPC471103
0.8599	High Similarity	NPC51602
0.8589	High Similarity	NPC471493
0.858	High Similarity	NPC478124
0.8562	High Similarity	NPC477735
0.8553	High Similarity	NPC282239
0.8545	High Similarity	NPC102465
0.8544	High Similarity	NPC283875
0.8544	High Similarity	NPC472548
0.8544	High Similarity	NPC22571
0.8544	High Similarity	NPC469647
0.8544	High Similarity	NPC469648
0.8544	High Similarity	NPC138641
0.8537	High Similarity	NPC477491
0.8535	High Similarity	NPC7095
0.8509	High Similarity	NPC477736
0.8509	High Similarity	NPC469399
0.8491	Intermediate Similarity	NPC469477
0.8491	Intermediate Similarity	NPC133430
0.8488	Intermediate Similarity	NPC186746
0.8471	Intermediate Similarity	NPC81698
0.8471	Intermediate Similarity	NPC250046
0.8471	Intermediate Similarity	NPC60509
0.8447	Intermediate Similarity	NPC472393
0.8447	Intermediate Similarity	NPC469417
0.8438	Intermediate Similarity	NPC26033
0.8438	Intermediate Similarity	NPC21410
0.8438	Intermediate Similarity	NPC473670
0.8438	Intermediate Similarity	NPC228204
0.8428	Intermediate Similarity	NPC477905
0.8428	Intermediate Similarity	NPC233581
0.8428	Intermediate Similarity	NPC145649
0.8418	Intermediate Similarity	NPC165260
0.8418	Intermediate Similarity	NPC112216
0.8418	Intermediate Similarity	NPC161239
0.8418	Intermediate Similarity	NPC198455
0.8415	Intermediate Similarity	NPC295408
0.8415	Intermediate Similarity	NPC329960
0.8415	Intermediate Similarity	NPC478125
0.8415	Intermediate Similarity	NPC150893
0.8397	Intermediate Similarity	NPC127857
0.8395	Intermediate Similarity	NPC319404
0.8395	Intermediate Similarity	NPC471102
0.8385	Intermediate Similarity	NPC217091
0.8383	Intermediate Similarity	NPC477488
0.8375	Intermediate Similarity	NPC229545
0.8375	Intermediate Similarity	NPC472030
0.8375	Intermediate Similarity	NPC134685
0.8375	Intermediate Similarity	NPC265395
0.8375	Intermediate Similarity	NPC257213
0.8375	Intermediate Similarity	NPC248265
0.8375	Intermediate Similarity	NPC256142
0.8375	Intermediate Similarity	NPC242262
0.8375	Intermediate Similarity	NPC219419
0.8375	Intermediate Similarity	NPC472005
0.8375	Intermediate Similarity	NPC304876
0.8375	Intermediate Similarity	NPC1173
0.8375	Intermediate Similarity	NPC249471
0.8375	Intermediate Similarity	NPC473414
0.8375	Intermediate Similarity	NPC237549
0.8375	Intermediate Similarity	NPC11588
0.8375	Intermediate Similarity	NPC472022
0.8375	Intermediate Similarity	NPC158333
0.8365	Intermediate Similarity	NPC62792
0.8365	Intermediate Similarity	NPC470153
0.8365	Intermediate Similarity	NPC306799
0.8365	Intermediate Similarity	NPC101043
0.8365	Intermediate Similarity	NPC298072
0.8354	Intermediate Similarity	NPC55744
0.8323	Intermediate Similarity	NPC473611
0.8323	Intermediate Similarity	NPC469730
0.8323	Intermediate Similarity	NPC132599
0.8323	Intermediate Similarity	NPC112523
0.8323	Intermediate Similarity	NPC114410
0.8323	Intermediate Similarity	NPC114357
0.8323	Intermediate Similarity	NPC155329
0.8323	Intermediate Similarity	NPC473632
0.8323	Intermediate Similarity	NPC259144
0.8302	Intermediate Similarity	NPC254558
0.8302	Intermediate Similarity	NPC476173
0.8302	Intermediate Similarity	NPC473214
0.8302	Intermediate Similarity	NPC470245
0.8302	Intermediate Similarity	NPC91730
0.8291	Intermediate Similarity	NPC132652
0.828	Intermediate Similarity	NPC471100
0.828	Intermediate Similarity	NPC471107
0.8274	Intermediate Similarity	NPC477471
0.8274	Intermediate Similarity	NPC477466
0.8274	Intermediate Similarity	NPC477473
0.8274	Intermediate Similarity	NPC477469
0.8261	Intermediate Similarity	NPC77719
0.8258	Intermediate Similarity	NPC77493
0.825	Intermediate Similarity	NPC478123
0.825	Intermediate Similarity	NPC197037
0.825	Intermediate Similarity	NPC469415
0.8239	Intermediate Similarity	NPC476975
0.8239	Intermediate Similarity	NPC473215
0.8235	Intermediate Similarity	NPC469421
0.8228	Intermediate Similarity	NPC240115
0.8228	Intermediate Similarity	NPC312393
0.8221	Intermediate Similarity	NPC469771
0.8217	Intermediate Similarity	NPC471139
0.8214	Intermediate Similarity	NPC469420
0.821	Intermediate Similarity	NPC469398
0.821	Intermediate Similarity	NPC34066
0.821	Intermediate Similarity	NPC469422
0.8194	Intermediate Similarity	NPC477904
0.8194	Intermediate Similarity	NPC183270
0.8187	Intermediate Similarity	NPC222102
0.8187	Intermediate Similarity	NPC303429
0.8176	Intermediate Similarity	NPC217918
0.8165	Intermediate Similarity	NPC174982
0.8165	Intermediate Similarity	NPC200471
0.8165	Intermediate Similarity	NPC472572
0.8165	Intermediate Similarity	NPC470159
0.8165	Intermediate Similarity	NPC70403
0.8165	Intermediate Similarity	NPC96903
0.8165	Intermediate Similarity	NPC476973
0.8165	Intermediate Similarity	NPC29704
0.8165	Intermediate Similarity	NPC184817
0.8165	Intermediate Similarity	NPC473088
0.8165	Intermediate Similarity	NPC158663
0.8165	Intermediate Similarity	NPC177940
0.8165	Intermediate Similarity	NPC171525
0.8165	Intermediate Similarity	NPC472571
0.8165	Intermediate Similarity	NPC469349
0.8165	Intermediate Similarity	NPC472575
0.8165	Intermediate Similarity	NPC472568
0.8165	Intermediate Similarity	NPC470157
0.8165	Intermediate Similarity	NPC471104
0.816	Intermediate Similarity	NPC70344
0.8153	Intermediate Similarity	NPC95449
0.8153	Intermediate Similarity	NPC477894
0.8148	Intermediate Similarity	NPC472657
0.8148	Intermediate Similarity	NPC472658
0.8141	Intermediate Similarity	NPC27377
0.8141	Intermediate Similarity	NPC291599
0.8141	Intermediate Similarity	NPC41481
0.8141	Intermediate Similarity	NPC213567
0.8141	Intermediate Similarity	NPC118080
0.8141	Intermediate Similarity	NPC87448
0.8141	Intermediate Similarity	NPC472576
0.8141	Intermediate Similarity	NPC16912
0.8141	Intermediate Similarity	NPC97947
0.8121	Intermediate Similarity	NPC477623
0.8113	Intermediate Similarity	NPC469513
0.8113	Intermediate Similarity	NPC474935
0.8113	Intermediate Similarity	NPC170668
0.8113	Intermediate Similarity	NPC473602
0.8101	Intermediate Similarity	NPC95265
0.8101	Intermediate Similarity	NPC163719
0.8101	Intermediate Similarity	NPC188865
0.8101	Intermediate Similarity	NPC475122
0.8101	Intermediate Similarity	NPC475759
0.8101	Intermediate Similarity	NPC25768
0.8101	Intermediate Similarity	NPC11685
0.8101	Intermediate Similarity	NPC241951
0.8101	Intermediate Similarity	NPC34943
0.8101	Intermediate Similarity	NPC472569
0.8101	Intermediate Similarity	NPC57628
0.8101	Intermediate Similarity	NPC470152
0.8101	Intermediate Similarity	NPC70716
0.8101	Intermediate Similarity	NPC125106
0.8101	Intermediate Similarity	NPC472573
0.8101	Intermediate Similarity	NPC95810

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 NPC322420 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	295
0.1-0.2	792
0.2-0.3	1686
0.3-0.4	3035
0.4-0.5	2236
0.5-0.6	863
0.6-0.7	209
0.7-0.8	33
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
0.8225	Intermediate Similarity	NPD7799	Discontinued
0.8057	Intermediate Similarity	NPD8055	Clinical (unspecified phase)
0.8	Intermediate Similarity	NPD8407	Phase 2
0.7931	Intermediate Similarity	NPD8368	Discontinued
0.7806	Intermediate Similarity	NPD7966	Clinical (unspecified phase)
0.7716	Intermediate Similarity	NPD7236	Approved
0.7657	Intermediate Similarity	NPD8470	Clinical (unspecified phase)
0.7624	Intermediate Similarity	NPD8360	Approved
0.7624	Intermediate Similarity	NPD8361	Approved
0.7624	Intermediate Similarity	NPD8435	Approved
0.7611	Intermediate Similarity	NPD8434	Phase 2
0.759	Intermediate Similarity	NPD7239	Suspended
0.7514	Intermediate Similarity	NPD8150	Discontinued
0.7446	Intermediate Similarity	NPD7879	Clinical (unspecified phase)
0.7418	Intermediate Similarity	NPD8424	Clinical (unspecified phase)
0.7354	Intermediate Similarity	NPD8486	Clinical (unspecified phase)
0.7238	Intermediate Similarity	NPD7685	Pre-registration
0.7196	Intermediate Similarity	NPD8485	Approved
0.7184	Intermediate Similarity	NPD7058	Phase 2
0.7184	Intermediate Similarity	NPD7057	Phase 3
0.7111	Intermediate Similarity	NPD3751	Discontinued
0.7068	Intermediate Similarity	NPD7699	Phase 2
0.7068	Intermediate Similarity	NPD7700	Phase 2
0.7059	Intermediate Similarity	NPD8397	Clinical (unspecified phase)
0.7035	Intermediate Similarity	NPD8462	Phase 1
0.7026	Intermediate Similarity	NPD8320	Phase 1
0.7026	Intermediate Similarity	NPD8319	Approved
0.7	Intermediate Similarity	NPD6534	Approved
0.7	Intermediate Similarity	NPD6535	Approved
0.6983	Remote Similarity	NPD3787	Discontinued
0.6978	Remote Similarity	NPD7804	Clinical (unspecified phase)
0.6974	Remote Similarity	NPD7435	Discontinued
0.6973	Remote Similarity	NPD8312	Approved
0.6973	Remote Similarity	NPD8313	Approved
0.6971	Remote Similarity	NPD7096	Clinical (unspecified phase)
0.6957	Remote Similarity	NPD5952	Clinical (unspecified phase)
0.6949	Remote Similarity	NPD7075	Discontinued
0.6919	Remote Similarity	NPD4338	Clinical (unspecified phase)
0.691	Remote Similarity	NPD5537	Clinical (unspecified phase)
0.6901	Remote Similarity	NPD8389	Clinical (unspecified phase)
0.6875	Remote Similarity	NPD7819	Suspended
0.6854	Remote Similarity	NPD4381	Clinical (unspecified phase)
0.685	Remote Similarity	NPD7875	Clinical (unspecified phase)
0.685	Remote Similarity	NPD7874	Approved
0.6831	Remote Similarity	NPD7228	Approved
0.6831	Remote Similarity	NPD3818	Discontinued
0.6828	Remote Similarity	NPD7808	Phase 3
0.6824	Remote Similarity	NPD6190	Approved
0.6821	Remote Similarity	NPD6782	Approved
0.6821	Remote Similarity	NPD6777	Approved
0.6821	Remote Similarity	NPD6781	Approved
0.6821	Remote Similarity	NPD6780	Approved
0.6821	Remote Similarity	NPD6778	Approved
0.6821	Remote Similarity	NPD6779	Approved
0.6821	Remote Similarity	NPD6776	Approved
0.6814	Remote Similarity	NPD8404	Phase 2
0.6802	Remote Similarity	NPD7697	Approved
0.6802	Remote Similarity	NPD7696	Phase 3
0.6802	Remote Similarity	NPD7698	Approved
0.68	Remote Similarity	NPD4380	Phase 2
0.6798	Remote Similarity	NPD4967	Phase 2
0.6798	Remote Similarity	NPD4965	Approved
0.6798	Remote Similarity	NPD4966	Approved
0.6778	Remote Similarity	NPD5494	Approved
0.6774	Remote Similarity	NPD7251	Discontinued
0.6774	Remote Similarity	NPD6559	Discontinued
0.6774	Remote Similarity	NPD6765	Approved
0.6774	Remote Similarity	NPD6764	Approved
0.677	Remote Similarity	NPD6007	Clinical (unspecified phase)
0.6768	Remote Similarity	NPD7870	Phase 2
0.6768	Remote Similarity	NPD7871	Phase 2
0.6757	Remote Similarity	NPD7074	Phase 3
0.6752	Remote Similarity	NPD5126	Approved
0.6752	Remote Similarity	NPD5125	Phase 3
0.675	Remote Similarity	NPD7701	Phase 2
0.6742	Remote Similarity	NPD5402	Approved
0.6733	Remote Similarity	NPD7801	Approved
0.6723	Remote Similarity	NPD6801	Discontinued
0.6723	Remote Similarity	NPD37	Approved
0.6722	Remote Similarity	NPD6234	Discontinued
0.672	Remote Similarity	NPD7993	Clinical (unspecified phase)
0.672	Remote Similarity	NPD6797	Phase 2
0.6703	Remote Similarity	NPD7054	Approved
0.6703	Remote Similarity	NPD5844	Phase 1
0.6685	Remote Similarity	NPD5761	Phase 2
0.6685	Remote Similarity	NPD7473	Discontinued
0.6685	Remote Similarity	NPD5760	Phase 2
0.6684	Remote Similarity	NPD7240	Approved
0.6667	Remote Similarity	NPD7472	Approved
0.6667	Remote Similarity	NPD7961	Discontinued
0.6667	Remote Similarity	NPD7184	Clinical (unspecified phase)
0.665	Remote Similarity	NPD7999	Approved
0.665	Remote Similarity	NPD7211	Clinical (unspecified phase)
0.6648	Remote Similarity	NPD3817	Phase 2
0.6648	Remote Similarity	NPD7199	Phase 2
0.6634	Remote Similarity	NPD7930	Approved
0.6632	Remote Similarity	NPD6784	Approved
0.6632	Remote Similarity	NPD6785	Approved
0.663	Remote Similarity	NPD6167	Clinical (unspecified phase)
0.663	Remote Similarity	NPD6166	Phase 2
0.663	Remote Similarity	NPD6168	Clinical (unspecified phase)
0.6611	Remote Similarity	NPD4868	Clinical (unspecified phase)
0.661	Remote Similarity	NPD6599	Discontinued
0.6609	Remote Similarity	NPD2532	Approved
0.6609	Remote Similarity	NPD2533	Approved
0.6609	Remote Similarity	NPD2534	Approved
0.6604	Remote Similarity	NPD7457	Clinical (unspecified phase)
0.6582	Remote Similarity	NPD8517	Approved
0.6582	Remote Similarity	NPD8516	Approved
0.6582	Remote Similarity	NPD8515	Approved
0.6582	Remote Similarity	NPD8513	Phase 3
0.657	Remote Similarity	NPD4628	Phase 3
0.6557	Remote Similarity	NPD8127	Discontinued
0.6556	Remote Similarity	NPD8443	Clinical (unspecified phase)
0.6554	Remote Similarity	NPD7458	Discontinued
0.6552	Remote Similarity	NPD8151	Discontinued
0.6552	Remote Similarity	NPD6799	Approved
0.655	Remote Similarity	NPD7497	Discontinued
0.6543	Remote Similarity	NPD7736	Approved
0.6536	Remote Similarity	NPD2181	Clinical (unspecified phase)
0.6534	Remote Similarity	NPD6980	Clinical (unspecified phase)
0.6534	Remote Similarity	NPD5403	Approved
0.6524	Remote Similarity	NPD8155	Clinical (unspecified phase)
0.6522	Remote Similarity	NPD6232	Discontinued
0.6519	Remote Similarity	NPD3882	Suspended
0.6517	Remote Similarity	NPD7028	Phase 2
0.6514	Remote Similarity	NPD5401	Approved
0.6513	Remote Similarity	NPD6214	Clinical (unspecified phase)
0.6513	Remote Similarity	NPD6212	Phase 3
0.6513	Remote Similarity	NPD6213	Phase 3
0.6503	Remote Similarity	NPD7319	Approved
0.65	Remote Similarity	NPD6823	Phase 2
0.65	Remote Similarity	NPD8455	Phase 2
0.65	Remote Similarity	NPD2393	Clinical (unspecified phase)
0.6491	Remote Similarity	NPD7266	Discontinued
0.648	Remote Similarity	NPD7411	Suspended
0.6474	Remote Similarity	NPD2575	Approved
0.6474	Remote Similarity	NPD1878	Clinical (unspecified phase)
0.6474	Remote Similarity	NPD8166	Discontinued
0.6474	Remote Similarity	NPD2629	Approved
0.6462	Remote Similarity	NPD5619	Clinical (unspecified phase)
0.6461	Remote Similarity	NPD6591	Clinical (unspecified phase)
0.646	Remote Similarity	NPD7492	Approved
0.6457	Remote Similarity	NPD6143	Clinical (unspecified phase)
0.6444	Remote Similarity	NPD1934	Approved
0.642	Remote Similarity	NPD6616	Approved
0.6415	Remote Similarity	NPD6054	Approved
0.6408	Remote Similarity	NPD7783	Phase 2
0.6408	Remote Similarity	NPD7782	Clinical (unspecified phase)
0.6407	Remote Similarity	NPD3764	Approved
0.64	Remote Similarity	NPD3300	Phase 2
0.6395	Remote Similarity	NPD2346	Discontinued
0.6393	Remote Similarity	NPD3749	Approved
0.6391	Remote Similarity	NPD230	Phase 1
0.638	Remote Similarity	NPD7078	Approved
0.6369	Remote Similarity	NPD3226	Approved
0.6369	Remote Similarity	NPD690	Clinical (unspecified phase)
0.6368	Remote Similarity	NPD7907	Approved
0.6364	Remote Similarity	NPD7852	Clinical (unspecified phase)
0.6351	Remote Similarity	NPD4111	Phase 1
0.6335	Remote Similarity	NPD6370	Approved
0.6335	Remote Similarity	NPD3412	Clinical (unspecified phase)
0.6329	Remote Similarity	NPD7115	Discovery
0.6329	Remote Similarity	NPD4198	Discontinued
0.6328	Remote Similarity	NPD4378	Clinical (unspecified phase)
0.6323	Remote Similarity	NPD4141	Clinical (unspecified phase)
0.6319	Remote Similarity	NPD7507	Approved
0.6319	Remote Similarity	NPD2801	Approved
0.6312	Remote Similarity	NPD7741	Discontinued
0.6301	Remote Similarity	NPD5763	Approved
0.6301	Remote Similarity	NPD5762	Approved
0.6299	Remote Similarity	NPD2182	Approved
0.6296	Remote Similarity	NPD8328	Phase 3
0.6292	Remote Similarity	NPD6273	Approved
0.629	Remote Similarity	NPD6959	Discontinued
0.6286	Remote Similarity	NPD6398	Clinical (unspecified phase)
0.6282	Remote Similarity	NPD1609	Clinical (unspecified phase)
0.6282	Remote Similarity	NPD969	Suspended
0.628	Remote Similarity	NPD8074	Phase 3
0.628	Remote Similarity	NPD8293	Discontinued
0.6279	Remote Similarity	NPD2799	Discontinued
0.6275	Remote Similarity	NPD7899	Clinical (unspecified phase)
0.6274	Remote Similarity	NPD4665	Approved
0.6273	Remote Similarity	NPD6016	Approved
0.6273	Remote Similarity	NPD6015	Approved
0.627	Remote Similarity	NPD919	Approved
0.6269	Remote Similarity	NPD8285	Discontinued
0.6265	Remote Similarity	NPD6085	Phase 2
0.6265	Remote Similarity	NPD5740	Clinical (unspecified phase)
0.6264	Remote Similarity	NPD970	Clinical (unspecified phase)
0.6257	Remote Similarity	NPD5710	Approved
0.6257	Remote Similarity	NPD5711	Approved
0.625	Remote Similarity	NPD5030	Phase 2
0.625	Remote Similarity	NPD7274	Clinical (unspecified phase)
0.625	Remote Similarity	NPD7008	Discontinued
0.625	Remote Similarity	NPD7768	Phase 2
0.6236	Remote Similarity	NPD7004	Clinical (unspecified phase)
0.6236	Remote Similarity	NPD7410	Clinical (unspecified phase)
0.6235	Remote Similarity	NPD5988	Approved
0.6234	Remote Similarity	NPD5345	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