NPASS Compound

Structure

NPC471654 OpenBabel07101719522D 44 49 0 0 1 0 0 0 0 0999 V2000 -0.3847 4.3218 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3147 -2.3364 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0794 2.3218 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5794 3.1878 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7788 -0.3364 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.2788 -1.2024 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4813 1.8218 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1808 0.1636 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2134 0.8218 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9128 1.1636 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3473 4.3218 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0468 -2.3364 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2507 2.8218 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4487 -0.8364 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3847 2.3218 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3147 -0.3364 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2134 3.8218 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9128 -1.8364 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0794 1.3218 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.7788 0.6636 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3473 1.3218 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0468 0.6636 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0303 2.7285 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6691 -0.7431 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4813 3.8218 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1808 -1.8364 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1168 2.3218 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5827 -0.3364 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4813 2.8218 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.1808 -0.8364 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.2134 2.8218 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.9128 -0.8364 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.2213 1.3272 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4781 0.6581 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1994 1.1193 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5000 0.8660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0794 2.3218 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.7788 -0.3364 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3473 2.3218 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.0468 -0.3364 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.6062 0.2058 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0933 1.7796 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.6994 1.9854 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 25 2 0 0 0 0 2 26 2 0 0 0 0 3 37 1 0 0 0 0 4 37 1 0 0 0 0 5 38 1 0 0 0 0 6 38 1 0 0 0 0 9 19 1 0 0 0 0 9 21 1 0 0 0 0 10 20 1 0 0 0 0 10 22 1 0 0 0 0 11 17 1 0 0 0 0 11 25 1 0 0 0 0 12 18 1 0 0 0 0 12 26 1 0 0 0 0 13 15 2 0 0 0 0 13 27 1 0 0 0 0 14 16 2 0 0 0 0 14 28 1 0 0 0 0 15 29 1 0 0 0 0 16 30 1 0 0 0 0 17 31 1 0 0 0 0 18 32 1 0 0 0 0 19 37 1 0 0 0 0 20 38 1 0 0 0 0 21 39 1 0 0 0 0 22 40 1 0 0 0 0 23 27 1 0 0 0 0 23 43 1 0 0 0 0 24 28 1 0 0 0 0 24 44 1 0 0 0 0 25 29 1 0 0 0 0 26 30 1 0 0 0 0 27 33 2 0 0 0 0 28 34 2 0 0 0 0 29 39 1 1 0 0 0 30 40 1 1 0 0 0 31 37 1 0 0 0 0 31 39 1 1 0 0 0 32 38 1 0 0 0 0 32 40 1 1 0 0 0 33 34 1 0 0 0 0 33 35 1 0 0 0 0 34 36 1 0 0 0 0 35 41 2 0 0 0 0 35 43 1 0 0 0 0 36 42 2 0 0 0 0 36 44 1 0 0 0 0 39 7 1 1 0 0 0 40 8 1 1 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	598.4
Volume:	663.126
LogP:	9.545
LogD:	6.417
LogS:	-5.667
# Rotatable Bonds:	5
TPSA:	66.74
# H-Bond Aceptor:	4
# H-Bond Donor:	2
# Rings:	6
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.336
Synthetic Accessibility Score:	5.466
Fsp3:	0.6
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Rejected
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:	-5.322
MDCK Permeability:	1.4061471119930502e-05
Pgp-inhibitor:	0.99
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.006
20% Bioavailability (F20%):	0.013
30% Bioavailability (F30%):	0.802

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.008
Plasma Protein Binding (PPB):	93.51707458496094%
Volume Distribution (VD):	4.212
Pgp-substrate:	1.3521069288253784%

ADMET: Metabolism

CYP1A2-inhibitor:	0.09
CYP1A2-substrate:	0.144
CYP2C19-inhibitor:	0.109
CYP2C19-substrate:	0.093
CYP2C9-inhibitor:	0.185
CYP2C9-substrate:	0.432
CYP2D6-inhibitor:	0.318
CYP2D6-substrate:	0.88
CYP3A4-inhibitor:	0.352
CYP3A4-substrate:	0.346

ADMET: Excretion

Clearance (CL):	8.969
Half-life (T1/2):	0.004

ADMET: Toxicity

hERG Blockers:	0.228
Human Hepatotoxicity (H-HT):	0.527
Drug-inuced Liver Injury (DILI):	0.047
AMES Toxicity:	0.01
Rat Oral Acute Toxicity:	0.964
Maximum Recommended Daily Dose:	0.886
Skin Sensitization:	0.382
Carcinogencity:	0.822
Eye Corrosion:	0.003
Eye Irritation:	0.008
Respiratory Toxicity:	0.851

Download Data

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

Natural Product: NPC471654

Natural Product ID:	NPC471654
*Common Name:**	Pahangensin A
IUPAC Name:	3-[(E)-2-[(1S,4aS,8aS)-5,5,8a-trimethyl-2-methylidene-3,4,4a,6,7,8-hexahydro-1H-naphthalen-1-yl]ethenyl]-4-[3-[(E)-2-[(1S,4aS,8aS)-5,5,8a-trimethyl-2-methylidene-3,4,4a,6,7,8-hexahydro-1H-naphthalen-1-yl]ethenyl]-5-oxo-2H-furan-4-yl]-2H-furan-5-one
Synonyms:
Standard InCHIKey:	FZNYZIIFIIKWRM-OLYZYIJMSA-N
Standard InCHI:	InChI=1S/C40H54O4/c1-25-11-17-31-37(3,4)19-9-21-39(31,7)29(25)15-13-27-23-43-35(41)33(27)34-28(24-44-36(34)42)14-16-30-26(2)12-18-32-38(5,6)20-10-22-40(30,32)8/h13-16,29-32H,1-2,9-12,17-24H2,3-8H3/b15-13+,16-14+/t29-,30-,31-,32-,39+,40+/m0/s1
SMILES:	C=C1CC[C@@H]2[C@]([C@H]1/C=C/C1=C(C(=O)OC1)C1=C(/C=C/[C@H]3C(=C)CC[C@@H]4[C@]3(C)CCCC4(C)C)COC1=O)(C)CCCC2(C)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL3087228
PubChem CID:	72543920
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001283] Terpene lactones [CHEMONTID:0001538] Diterpene lactones

*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
NPO32724	Alpinia pahangensis	Species	Zingiberaceae	Eukaryota	rhizomes	n.a.	n.a.	PMID[24144849]

☑ 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
MIC	3

Activity Type	# Activity
Organism	3

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	=	52.08	ug.mL-1	PMID[528959]
NPT314	Organism	Bacillus cereus	Bacillus cereus	MIC	=	31.25	ug.mL-1	PMID[528959]
NPT79	Organism	Bacillus subtilis	Bacillus subtilis	MIC	=	31.25	ug.mL-1	PMID[528959]

☑ 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 NPC471654 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	219
0.1-0.2	1371
0.2-0.3	5706
0.3-0.4	16420
0.4-0.5	9198
0.5-0.6	7857
0.6-0.7	1843
0.7-0.8	82
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
0.8214	Intermediate Similarity	NPC4509
0.8	Intermediate Similarity	NPC30984
0.7865	Intermediate Similarity	NPC94200
0.7778	Intermediate Similarity	NPC469
0.7667	Intermediate Similarity	NPC16321
0.7667	Intermediate Similarity	NPC268122
0.766	Intermediate Similarity	NPC474844
0.7582	Intermediate Similarity	NPC118423
0.7579	Intermediate Similarity	NPC159748
0.7579	Intermediate Similarity	NPC101651
0.7527	Intermediate Similarity	NPC168248
0.75	Intermediate Similarity	NPC477720
0.75	Intermediate Similarity	NPC318515
0.7475	Intermediate Similarity	NPC257726
0.7475	Intermediate Similarity	NPC204054
0.7474	Intermediate Similarity	NPC284561
0.7473	Intermediate Similarity	NPC200513
0.7442	Intermediate Similarity	NPC144947
0.7419	Intermediate Similarity	NPC329630
0.7419	Intermediate Similarity	NPC217394
0.7419	Intermediate Similarity	NPC474013
0.7396	Intermediate Similarity	NPC212679
0.7396	Intermediate Similarity	NPC469595
0.7396	Intermediate Similarity	NPC220454
0.7391	Intermediate Similarity	NPC474790
0.7391	Intermediate Similarity	NPC474976
0.7368	Intermediate Similarity	NPC196407
0.7368	Intermediate Similarity	NPC472302
0.7349	Intermediate Similarity	NPC185587
0.7347	Intermediate Similarity	NPC477129
0.7347	Intermediate Similarity	NPC477130
0.7312	Intermediate Similarity	NPC96055
0.73	Intermediate Similarity	NPC110937
0.7292	Intermediate Similarity	NPC177141
0.7283	Intermediate Similarity	NPC471218
0.7273	Intermediate Similarity	NPC209355
0.7263	Intermediate Similarity	NPC477228
0.7263	Intermediate Similarity	NPC163016
0.7263	Intermediate Similarity	NPC75315
0.7255	Intermediate Similarity	NPC63249
0.7253	Intermediate Similarity	NPC268827
0.7245	Intermediate Similarity	NPC205034
0.7245	Intermediate Similarity	NPC162615
0.7245	Intermediate Similarity	NPC152778
0.7234	Intermediate Similarity	NPC65661
0.7216	Intermediate Similarity	NPC221111
0.7216	Intermediate Similarity	NPC273199
0.7216	Intermediate Similarity	NPC469372
0.7216	Intermediate Similarity	NPC182136
0.7216	Intermediate Similarity	NPC310479
0.7216	Intermediate Similarity	NPC280149
0.7212	Intermediate Similarity	NPC189616
0.7204	Intermediate Similarity	NPC42476
0.72	Intermediate Similarity	NPC16967
0.7188	Intermediate Similarity	NPC226863
0.7188	Intermediate Similarity	NPC473879
0.7184	Intermediate Similarity	NPC134077
0.7172	Intermediate Similarity	NPC476415
0.7143	Intermediate Similarity	NPC190211
0.7129	Intermediate Similarity	NPC121402
0.7129	Intermediate Similarity	NPC151681
0.7129	Intermediate Similarity	NPC132753
0.7129	Intermediate Similarity	NPC224356
0.7129	Intermediate Similarity	NPC175351
0.7128	Intermediate Similarity	NPC470800
0.7126	Intermediate Similarity	NPC257618
0.7115	Intermediate Similarity	NPC254202
0.7113	Intermediate Similarity	NPC174342
0.7108	Intermediate Similarity	NPC329698
0.71	Intermediate Similarity	NPC281134
0.71	Intermediate Similarity	NPC33473
0.71	Intermediate Similarity	NPC295347
0.71	Intermediate Similarity	NPC474909
0.7097	Intermediate Similarity	NPC15910
0.7087	Intermediate Similarity	NPC168319
0.7087	Intermediate Similarity	NPC194028
0.7083	Intermediate Similarity	NPC125925
0.7071	Intermediate Similarity	NPC151722
0.7071	Intermediate Similarity	NPC169343
0.7071	Intermediate Similarity	NPC475657
0.7071	Intermediate Similarity	NPC242069
0.7071	Intermediate Similarity	NPC469939
0.7071	Intermediate Similarity	NPC1108
0.7053	Intermediate Similarity	NPC189311
0.7053	Intermediate Similarity	NPC106416
0.7053	Intermediate Similarity	NPC86316
0.7045	Intermediate Similarity	NPC16349
0.7045	Intermediate Similarity	NPC222244
0.7041	Intermediate Similarity	NPC8062
0.7041	Intermediate Similarity	NPC302280
0.7033	Intermediate Similarity	NPC105197
0.7033	Intermediate Similarity	NPC184737
0.703	Intermediate Similarity	NPC112654
0.703	Intermediate Similarity	NPC472362
0.703	Intermediate Similarity	NPC154526
0.703	Intermediate Similarity	NPC472363
0.703	Intermediate Similarity	NPC325960
0.703	Intermediate Similarity	NPC473153
0.703	Intermediate Similarity	NPC319692
0.7021	Intermediate Similarity	NPC474193
0.7021	Intermediate Similarity	NPC22611
0.7021	Intermediate Similarity	NPC12283
0.7021	Intermediate Similarity	NPC477124
0.7021	Intermediate Similarity	NPC472440
0.7019	Intermediate Similarity	NPC273668
0.7019	Intermediate Similarity	NPC155332
0.7019	Intermediate Similarity	NPC32577
0.7019	Intermediate Similarity	NPC114540
0.701	Intermediate Similarity	NPC93411
0.701	Intermediate Similarity	NPC477128
0.701	Intermediate Similarity	NPC474629
0.7	Intermediate Similarity	NPC470255
0.7	Intermediate Similarity	NPC88507
0.7	Intermediate Similarity	NPC84893
0.7	Intermediate Similarity	NPC191521
0.7	Intermediate Similarity	NPC477722
0.699	Remote Similarity	NPC474190
0.6989	Remote Similarity	NPC14203
0.6989	Remote Similarity	NPC229584
0.6989	Remote Similarity	NPC40228
0.6979	Remote Similarity	NPC220478
0.6979	Remote Similarity	NPC118266
0.697	Remote Similarity	NPC72845
0.697	Remote Similarity	NPC329842
0.697	Remote Similarity	NPC65513
0.6966	Remote Similarity	NPC20025
0.6966	Remote Similarity	NPC168975
0.6966	Remote Similarity	NPC75485
0.6961	Remote Similarity	NPC10057
0.6961	Remote Similarity	NPC100912
0.6961	Remote Similarity	NPC84335
0.6961	Remote Similarity	NPC38530
0.6961	Remote Similarity	NPC51499
0.6961	Remote Similarity	NPC476768
0.6961	Remote Similarity	NPC208094
0.6957	Remote Similarity	NPC471299
0.6952	Remote Similarity	NPC180204
0.6947	Remote Similarity	NPC312660
0.6947	Remote Similarity	NPC149869
0.6947	Remote Similarity	NPC475100
0.6944	Remote Similarity	NPC228477
0.6944	Remote Similarity	NPC137911
0.6939	Remote Similarity	NPC79027
0.6939	Remote Similarity	NPC474396
0.6939	Remote Similarity	NPC168131
0.6939	Remote Similarity	NPC285982
0.6939	Remote Similarity	NPC475049
0.6939	Remote Similarity	NPC50488
0.6939	Remote Similarity	NPC293044
0.6932	Remote Similarity	NPC181587
0.6931	Remote Similarity	NPC280877
0.6931	Remote Similarity	NPC127197
0.6931	Remote Similarity	NPC293052
0.6923	Remote Similarity	NPC473825
0.6923	Remote Similarity	NPC473160
0.6923	Remote Similarity	NPC476888
0.6923	Remote Similarity	NPC93744
0.6923	Remote Similarity	NPC54996
0.6923	Remote Similarity	NPC189206
0.6923	Remote Similarity	NPC310981
0.6915	Remote Similarity	NPC186276
0.6915	Remote Similarity	NPC324170
0.6907	Remote Similarity	NPC476600
0.6905	Remote Similarity	NPC226066
0.69	Remote Similarity	NPC53555
0.69	Remote Similarity	NPC476416
0.69	Remote Similarity	NPC472303
0.6893	Remote Similarity	NPC474440
0.6893	Remote Similarity	NPC98868
0.6893	Remote Similarity	NPC473154
0.6893	Remote Similarity	NPC72647
0.6893	Remote Similarity	NPC107806
0.6893	Remote Similarity	NPC275086
0.6893	Remote Similarity	NPC176845
0.6893	Remote Similarity	NPC325229
0.6889	Remote Similarity	NPC65650
0.6889	Remote Similarity	NPC228978
0.6882	Remote Similarity	NPC195424
0.6881	Remote Similarity	NPC16270
0.6875	Remote Similarity	NPC471795
0.6875	Remote Similarity	NPC472442
0.6875	Remote Similarity	NPC2709
0.6869	Remote Similarity	NPC51486
0.6869	Remote Similarity	NPC198818
0.6869	Remote Similarity	NPC78973
0.6869	Remote Similarity	NPC471818
0.6869	Remote Similarity	NPC76286
0.6869	Remote Similarity	NPC477782
0.6863	Remote Similarity	NPC260796
0.6863	Remote Similarity	NPC311166
0.6857	Remote Similarity	NPC476890
0.6857	Remote Similarity	NPC273005
0.6857	Remote Similarity	NPC469606
0.6857	Remote Similarity	NPC165250
0.6857	Remote Similarity	NPC283343
0.6857	Remote Similarity	NPC258547
0.6857	Remote Similarity	NPC476081
0.6857	Remote Similarity	NPC40918
0.6857	Remote Similarity	NPC31058
0.6854	Remote Similarity	NPC276336

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 NPC471654 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	188
0.1-0.2	1325
0.2-0.3	4308
0.3-0.4	2476
0.4-0.5	575
0.5-0.6	233
0.6-0.7	41
0.7-0.8	4
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
0.7473	Intermediate Similarity	NPD4752	Clinical (unspecified phase)
0.7172	Intermediate Similarity	NPD7901	Clinical (unspecified phase)
0.7172	Intermediate Similarity	NPD7900	Approved
0.6961	Remote Similarity	NPD7902	Approved
0.6905	Remote Similarity	NPD5325	Clinical (unspecified phase)
0.6889	Remote Similarity	NPD8039	Approved
0.6731	Remote Similarity	NPD7638	Approved
0.6667	Remote Similarity	NPD7513	Clinical (unspecified phase)
0.6667	Remote Similarity	NPD7748	Approved
0.6667	Remote Similarity	NPD7640	Approved
0.6667	Remote Similarity	NPD7639	Approved
0.6634	Remote Similarity	NPD7637	Suspended
0.6571	Remote Similarity	NPD4225	Approved
0.6569	Remote Similarity	NPD6399	Phase 3
0.6562	Remote Similarity	NPD5209	Approved
0.65	Remote Similarity	NPD5737	Approved
0.65	Remote Similarity	NPD6672	Approved
0.65	Remote Similarity	NPD6903	Approved
0.6471	Remote Similarity	NPD8034	Phase 2
0.6471	Remote Similarity	NPD8035	Phase 2
0.6465	Remote Similarity	NPD7146	Approved
0.6465	Remote Similarity	NPD5330	Approved
0.6465	Remote Similarity	NPD7521	Approved
0.6465	Remote Similarity	NPD6684	Approved
0.6465	Remote Similarity	NPD7334	Approved
0.6465	Remote Similarity	NPD6409	Approved
0.6436	Remote Similarity	NPD6051	Approved
0.6429	Remote Similarity	NPD6400	Clinical (unspecified phase)
0.6415	Remote Similarity	NPD8029	Clinical (unspecified phase)
0.6396	Remote Similarity	NPD6686	Approved
0.6373	Remote Similarity	NPD5207	Approved
0.6364	Remote Similarity	NPD1694	Approved
0.6311	Remote Similarity	NPD7515	Phase 2
0.6311	Remote Similarity	NPD5693	Phase 1
0.6286	Remote Similarity	NPD6356	Clinical (unspecified phase)
0.6275	Remote Similarity	NPD7285	Clinical (unspecified phase)
0.6239	Remote Similarity	NPD7115	Discovery
0.6237	Remote Similarity	NPD4058	Approved
0.6167	Remote Similarity	NPD8033	Approved
0.6161	Remote Similarity	NPD5954	Clinical (unspecified phase)
0.6154	Remote Similarity	NPD5281	Approved
0.6154	Remote Similarity	NPD6050	Approved
0.6154	Remote Similarity	NPD5284	Approved
0.6154	Remote Similarity	NPD5694	Approved
0.6117	Remote Similarity	NPD6673	Approved
0.6117	Remote Similarity	NPD6080	Approved
0.6117	Remote Similarity	NPD6904	Approved
0.6092	Remote Similarity	NPD4191	Approved
0.6092	Remote Similarity	NPD4194	Approved
0.6092	Remote Similarity	NPD4192	Approved
0.6092	Remote Similarity	NPD4193	Approved
0.6091	Remote Similarity	NPD7632	Discontinued
0.6083	Remote Similarity	NPD8294	Approved
0.6083	Remote Similarity	NPD8377	Approved
0.6078	Remote Similarity	NPD3573	Approved
0.6071	Remote Similarity	NPD6008	Approved
0.6064	Remote Similarity	NPD5733	Approved
0.6064	Remote Similarity	NPD4687	Approved
0.6058	Remote Similarity	NPD5785	Approved
0.6058	Remote Similarity	NPD7838	Discovery
0.6058	Remote Similarity	NPD5692	Phase 3
0.605	Remote Similarity	NPD7328	Approved
0.605	Remote Similarity	NPD7327	Approved
0.604	Remote Similarity	NPD6082	Clinical (unspecified phase)
0.6033	Remote Similarity	NPD8378	Approved
0.6033	Remote Similarity	NPD8296	Approved
0.6033	Remote Similarity	NPD8380	Approved
0.6033	Remote Similarity	NPD8335	Approved
0.6033	Remote Similarity	NPD8379	Approved
0.6022	Remote Similarity	NPD5276	Approved
0.6019	Remote Similarity	NPD6083	Phase 2
0.6019	Remote Similarity	NPD6084	Phase 2
0.6	Remote Similarity	NPD7516	Approved
0.6	Remote Similarity	NPD5955	Clinical (unspecified phase)
0.6	Remote Similarity	NPD6411	Approved
0.5981	Remote Similarity	NPD1698	Clinical (unspecified phase)
0.5978	Remote Similarity	NPD4137	Phase 3
0.5968	Remote Similarity	NPD7507	Approved
0.5963	Remote Similarity	NPD5696	Approved
0.5948	Remote Similarity	NPD6649	Approved
0.5948	Remote Similarity	NPD6650	Approved
0.5926	Remote Similarity	NPD7732	Phase 3
0.5914	Remote Similarity	NPD4691	Approved
0.5914	Remote Similarity	NPD4747	Approved
0.5913	Remote Similarity	NPD6373	Approved
0.5913	Remote Similarity	NPD6372	Approved
0.5909	Remote Similarity	NPD6648	Approved
0.5902	Remote Similarity	NPD7503	Approved
0.5889	Remote Similarity	NPD2685	Clinical (unspecified phase)
0.5888	Remote Similarity	NPD6001	Approved
0.5865	Remote Similarity	NPD5208	Approved
0.5859	Remote Similarity	NPD8259	Clinical (unspecified phase)
0.5847	Remote Similarity	NPD6858	Approved
0.5847	Remote Similarity	NPD7094	Approved
0.5833	Remote Similarity	NPD8264	Approved
0.5833	Remote Similarity	NPD5695	Phase 3
0.5827	Remote Similarity	NPD7319	Approved
0.5826	Remote Similarity	NPD6899	Approved
0.5826	Remote Similarity	NPD6881	Approved
0.5826	Remote Similarity	NPD7320	Approved
0.5825	Remote Similarity	NPD6098	Approved
0.5816	Remote Similarity	NPD7322	Clinical (unspecified phase)
0.5812	Remote Similarity	NPD8130	Phase 1
0.581	Remote Similarity	NPD5764	Clinical (unspecified phase)
0.581	Remote Similarity	NPD6101	Approved
0.5794	Remote Similarity	NPD5779	Approved
0.5794	Remote Similarity	NPD5778	Approved
0.5789	Remote Similarity	NPD6402	Approved
0.5789	Remote Similarity	NPD6675	Approved
0.5789	Remote Similarity	NPD7128	Approved
0.5789	Remote Similarity	NPD5739	Approved
0.5784	Remote Similarity	NPD7338	Clinical (unspecified phase)
0.5776	Remote Similarity	NPD4061	Clinical (unspecified phase)
0.5763	Remote Similarity	NPD6053	Discontinued
0.5763	Remote Similarity	NPD8297	Approved
0.5755	Remote Similarity	NPD6698	Approved
0.5755	Remote Similarity	NPD46	Approved
0.5752	Remote Similarity	NPD6052	Approved
0.5745	Remote Similarity	NPD7144	Approved
0.5745	Remote Similarity	NPD7143	Approved
0.5739	Remote Similarity	NPD5697	Approved
0.5728	Remote Similarity	NPD7520	Clinical (unspecified phase)
0.5726	Remote Similarity	NPD7102	Approved
0.5726	Remote Similarity	NPD7290	Approved
0.5726	Remote Similarity	NPD6883	Approved
0.57	Remote Similarity	NPD7332	Phase 2
0.57	Remote Similarity	NPD5790	Clinical (unspecified phase)
0.57	Remote Similarity	NPD7514	Phase 3
0.57	Remote Similarity	NPD4695	Discontinued
0.569	Remote Similarity	NPD6011	Approved
0.5688	Remote Similarity	NPD5654	Approved
0.5686	Remote Similarity	NPD5362	Discontinued
0.5686	Remote Similarity	NPD6695	Phase 3
0.5684	Remote Similarity	NPD7152	Approved
0.5684	Remote Similarity	NPD7151	Approved
0.5684	Remote Similarity	NPD7150	Approved
0.5682	Remote Similarity	NPD7961	Discontinued
0.5678	Remote Similarity	NPD6869	Approved
0.5678	Remote Similarity	NPD6847	Approved
0.5678	Remote Similarity	NPD6617	Approved
0.5673	Remote Similarity	NPD5279	Phase 3
0.5673	Remote Similarity	NPD4519	Discontinued
0.5673	Remote Similarity	NPD4623	Approved
0.5673	Remote Similarity	NPD3618	Phase 1
0.5663	Remote Similarity	NPD6927	Phase 3
0.5657	Remote Similarity	NPD7145	Approved
0.5657	Remote Similarity	NPD5784	Clinical (unspecified phase)
0.5644	Remote Similarity	NPD6902	Approved
0.5644	Remote Similarity	NPD8028	Phase 2
0.5641	Remote Similarity	NPD6012	Approved
0.5641	Remote Similarity	NPD6014	Approved
0.5641	Remote Similarity	NPD2182	Approved
0.5641	Remote Similarity	NPD6013	Approved
0.5638	Remote Similarity	NPD6922	Approved
0.5638	Remote Similarity	NPD6923	Approved
0.5631	Remote Similarity	NPD4786	Approved
0.5631	Remote Similarity	NPD3666	Approved
0.5631	Remote Similarity	NPD3665	Phase 1
0.5631	Remote Similarity	NPD3133	Approved
0.5631	Remote Similarity	NPD3668	Phase 3
0.563	Remote Similarity	NPD6882	Approved
0.5625	Remote Similarity	NPD6404	Discontinued
0.5619	Remote Similarity	NPD7750	Discontinued
0.5615	Remote Similarity	NPD7260	Phase 2
0.5603	Remote Similarity	NPD6412	Phase 2
0.5603	Remote Similarity	NPD6614	Approved
0.5603	Remote Similarity	NPD7899	Clinical (unspecified phase)
0.5603	Remote Similarity	NPD5701	Approved
0.56	Remote Similarity	NPD7645	Phase 2

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