NPASS Compound

Structure

CID163083 OpenBabel06191715532D 21 21 0 0 0 0 0 0 0 0999 V2000 6.9282 6.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 6.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 6.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 5.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 3 1 0 0 0 0 2 21 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 5 6 1 0 0 0 0 6 14 1 0 0 0 0 7 9 1 0 0 0 0 7 13 1 0 0 0 0 8 10 2 0 0 0 0 8 13 1 0 0 0 0 9 15 1 0 0 0 0 10 16 1 0 0 0 0 11 13 2 0 0 0 0 11 17 1 0 0 0 0 12 14 1 0 0 0 0 12 15 1 0 0 0 0 14 18 2 0 0 0 0 15 19 2 0 0 0 0 16 17 2 0 0 0 0 16 20 1 0 0 0 0 17 21 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	292.17
Volume:	316.01
LogP:	2.739
LogD:	2.466
LogS:	-2.723
# Rotatable Bonds:	10
TPSA:	63.6
# H-Bond Aceptor:	4
# H-Bond Donor:	1
# Rings:	1
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.53
Synthetic Accessibility Score:	2.146
Fsp3:	0.529
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	1
Golden Triangle Rule:	Accepted
Chelating Alert:	2
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.743
MDCK Permeability:	2.593293902464211e-05
Pgp-inhibitor:	0.936
Pgp-substrate:	0.481
Human Intestinal Absorption (HIA):	0.029
20% Bioavailability (F20%):	0.906
30% Bioavailability (F30%):	0.522

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.619
Plasma Protein Binding (PPB):	73.49742889404297%
Volume Distribution (VD):	0.8
Pgp-substrate:	12.930429458618164%

ADMET: Metabolism

CYP1A2-inhibitor:	0.733
CYP1A2-substrate:	0.937
CYP2C19-inhibitor:	0.872
CYP2C19-substrate:	0.525
CYP2C9-inhibitor:	0.818
CYP2C9-substrate:	0.93
CYP2D6-inhibitor:	0.259
CYP2D6-substrate:	0.889
CYP3A4-inhibitor:	0.619
CYP3A4-substrate:	0.239

ADMET: Excretion

Clearance (CL):	11.78
Half-life (T1/2):	0.942

ADMET: Toxicity

hERG Blockers:	0.052
Human Hepatotoxicity (H-HT):	0.114
Drug-inuced Liver Injury (DILI):	0.468
AMES Toxicity:	0.506
Rat Oral Acute Toxicity:	0.061
Maximum Recommended Daily Dose:	0.153
Skin Sensitization:	0.858
Carcinogencity:	0.038
Eye Corrosion:	0.83
Eye Irritation:	0.976
Respiratory Toxicity:	0.899

Download Data

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

Natural Product: NPC163083

Natural Product ID:	NPC163083
*Common Name:**	1-(4-Hydroxy-3-Methoxyphenyl)Decane-3,5-Dione
IUPAC Name:	1-(4-hydroxy-3-methoxyphenyl)decane-3,5-dione
Synonyms:	6-gingerdione
Standard InCHIKey:	KMNVXQHNIWUUSE-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C17H24O4/c1-3-4-5-6-14(18)12-15(19)9-7-13-8-10-16(20)17(11-13)21-2/h8,10-11,20H,3-7,9,12H2,1-2H3
SMILES:	CCCCCC(=O)CC(=O)CCc1ccc(c(c1)OC)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL2071439
PubChem CID:	162952
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0002448] Benzenoids [CHEMONTID:0000134] Phenols [CHEMONTID:0000190] Methoxyphenols [CHEMONTID:0001707] Gingerdiones

*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
NPO20553	Zingiber officinale	Species	Zingiberaceae	Eukaryota	rhizomes	n.a.	n.a.	PMID[18177011]
NPO20553	Zingiber officinale	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19271742]
NPO20553	Zingiber officinale	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20590154]
NPO19141	Aframomum melegueta	Species	Zingiberaceae	Eukaryota	Seeds	n.a.	n.a.	PMID[22789014]
NPO20553	Zingiber officinale	Species	Zingiberaceae	Eukaryota	n.a.	rhizome	n.a.	PMID[8064299]
NPO20553	Zingiber officinale	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[8064299]
NPO20553	Zingiber officinale	Species	Zingiberaceae	Eukaryota	n.a.	n.a.		Database[FooDB]
NPO20553	Zingiber officinale	Species	Zingiberaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO20553	Zingiber officinale	Species	Zingiberaceae	Eukaryota	Plant	n.a.	n.a.	Database[FooDB]
NPO20553	Zingiber officinale	Species	Zingiberaceae	Eukaryota	Resin, Exudate, Sap	n.a.	n.a.	Database[FooDB]
NPO20553	Zingiber officinale	Species	Zingiberaceae	Eukaryota	Rhizome	n.a.	n.a.	Database[FooDB]
NPO20553	Zingiber officinale	Species	Zingiberaceae	Eukaryota	Root	n.a.	n.a.	Database[FooDB]
NPO20553	Zingiber officinale	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO20553	Zingiber officinale	Species	Zingiberaceae	Eukaryota	n.a.	n.a.		Database[Phenol-Explorer]
NPO20553	Zingiber officinale	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO20553	Zingiber officinale	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO20553	Zingiber officinale	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO19141	Aframomum melegueta	Species	Zingiberaceae	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
MIC	2
Others	9

Activity Type	# Activity
Organism	2
Others	9

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT1107	Organism	Mycobacterium smegmatis str. MC2 155	Mycobacterium smegmatis str. MC2 155	MIC	>=	128.0	ug.mL-1	PMID[478652]
NPT1107	Organism	Mycobacterium smegmatis str. MC2 155	Mycobacterium smegmatis str. MC2 155	MIC	=	128.0	ug.mL-1	PMID[478652]
NPT2	Others	Unspecified		FC	=	8.0	n.a.	PMID[478652]
NPT2	Others	Unspecified		FC	=	2.0	n.a.	PMID[478652]
NPT2	Others	Unspecified		FC	=	1.0	n.a.	PMID[478652]
NPT2	Others	Unspecified		FC	=	4.0	n.a.	PMID[478652]
NPT2	Others	Unspecified		FICI	=	0.25	n.a.	PMID[478652]
NPT2	Others	Unspecified		FICI	=	0.5	n.a.	PMID[478652]
NPT2	Others	Unspecified		RFU	=	17766.4	n.a.	PMID[478652]
NPT2	Others	Unspecified		Ratio	=	0.789	n.a.	PMID[478652]

☑ 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 NPC163083 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	266
0.1-0.2	1383
0.2-0.3	4027
0.3-0.4	11683
0.4-0.5	6741
0.5-0.6	4439
0.6-0.7	9428
0.7-0.8	4222
0.8-0.85	334
0.85-0.9	115
0.9-0.95	51
0.95-1	8

Similarity Score	Similarity Level	Natural Product ID
0.9828	High Similarity	NPC201777
0.9748	High Similarity	NPC127937
0.9748	High Similarity	NPC92207
0.9664	High Similarity	NPC257589
0.9664	High Similarity	NPC53305
0.9569	High Similarity	NPC299406
0.9508	High Similarity	NPC304622
0.9504	High Similarity	NPC293641
0.9504	High Similarity	NPC12022
0.9504	High Similarity	NPC20287
0.9504	High Similarity	NPC20404
0.9496	High Similarity	NPC4181
0.9496	High Similarity	NPC242372
0.9496	High Similarity	NPC257976
0.9496	High Similarity	NPC164778
0.9426	High Similarity	NPC278308
0.9426	High Similarity	NPC226661
0.9421	High Similarity	NPC84076
0.9421	High Similarity	NPC90128
0.9421	High Similarity	NPC303680
0.9417	High Similarity	NPC273686
0.9417	High Similarity	NPC312404
0.9412	High Similarity	NPC114298
0.9407	High Similarity	NPC158949
0.9344	High Similarity	NPC123722
0.9344	High Similarity	NPC276466
0.9344	High Similarity	NPC151167
0.9344	High Similarity	NPC5018
0.9344	High Similarity	NPC123228
0.9339	High Similarity	NPC280767
0.9328	High Similarity	NPC194416
0.9328	High Similarity	NPC177291
0.9274	High Similarity	NPC244246
0.9274	High Similarity	NPC123196
0.9274	High Similarity	NPC137427
0.9274	High Similarity	NPC275724
0.9274	High Similarity	NPC311419
0.9274	High Similarity	NPC215941
0.9274	High Similarity	NPC172673
0.9274	High Similarity	NPC319282
0.9274	High Similarity	NPC65935
0.9262	High Similarity	NPC179777
0.918	High Similarity	NPC3221
0.9174	High Similarity	NPC244876
0.9127	High Similarity	NPC239302
0.912	High Similarity	NPC195292
0.912	High Similarity	NPC142985
0.9055	High Similarity	NPC327410
0.9048	High Similarity	NPC469480
0.9016	High Similarity	NPC160900
0.9016	High Similarity	NPC18984
0.9016	High Similarity	NPC106659
0.9016	High Similarity	NPC229084
0.8992	High Similarity	NPC205502
0.8992	High Similarity	NPC470626
0.8952	High Similarity	NPC276014
0.8934	High Similarity	NPC286573
0.8917	High Similarity	NPC311595
0.8917	High Similarity	NPC24474
0.8915	High Similarity	NPC152209
0.8908	High Similarity	NPC164386
0.8908	High Similarity	NPC293619
0.8889	High Similarity	NPC241354
0.888	High Similarity	NPC16651
0.888	High Similarity	NPC281020
0.888	High Similarity	NPC32163
0.8879	High Similarity	NPC257124
0.8879	High Similarity	NPC156840
0.8879	High Similarity	NPC8547
0.8879	High Similarity	NPC173746
0.8843	High Similarity	NPC95614
0.8843	High Similarity	NPC56214
0.8843	High Similarity	NPC232316
0.8843	High Similarity	NPC117780
0.8843	High Similarity	NPC165133
0.8843	High Similarity	NPC227217
0.8843	High Similarity	NPC242885
0.8837	High Similarity	NPC300776
0.8837	High Similarity	NPC176814
0.8837	High Similarity	NPC4982
0.8837	High Similarity	NPC68779
0.8837	High Similarity	NPC471110
0.8837	High Similarity	NPC5310
0.8819	High Similarity	NPC66905
0.8788	High Similarity	NPC474784
0.877	High Similarity	NPC207613
0.877	High Similarity	NPC189844
0.877	High Similarity	NPC109083
0.877	High Similarity	NPC269843
0.877	High Similarity	NPC224814
0.877	High Similarity	NPC14007
0.877	High Similarity	NPC60962
0.8769	High Similarity	NPC204592
0.8769	High Similarity	NPC113295
0.876	High Similarity	NPC310338
0.876	High Similarity	NPC281298
0.876	High Similarity	NPC475468
0.8707	High Similarity	NPC246358
0.8707	High Similarity	NPC7097
0.8707	High Similarity	NPC36108
0.8707	High Similarity	NPC233731
0.8702	High Similarity	NPC90431
0.8699	High Similarity	NPC54872
0.8699	High Similarity	NPC113865
0.8699	High Similarity	NPC184651
0.8699	High Similarity	NPC343720
0.8699	High Similarity	NPC262156
0.8699	High Similarity	NPC470212
0.8699	High Similarity	NPC312675
0.8699	High Similarity	NPC473853
0.8699	High Similarity	NPC160380
0.8699	High Similarity	NPC38996
0.8699	High Similarity	NPC324571
0.8682	High Similarity	NPC50763
0.8672	High Similarity	NPC477705
0.8672	High Similarity	NPC477694
0.8657	High Similarity	NPC472410
0.8647	High Similarity	NPC322021
0.864	High Similarity	NPC60517
0.864	High Similarity	NPC146886
0.864	High Similarity	NPC20443
0.8629	High Similarity	NPC85488
0.8626	High Similarity	NPC470990
0.8626	High Similarity	NPC252343
0.8618	High Similarity	NPC98305
0.8605	High Similarity	NPC477706
0.8582	High Similarity	NPC19158
0.8571	High Similarity	NPC284409
0.8571	High Similarity	NPC148969
0.856	High Similarity	NPC31344
0.856	High Similarity	NPC280704
0.856	High Similarity	NPC317769
0.856	High Similarity	NPC471693
0.8559	High Similarity	NPC78918
0.8559	High Similarity	NPC195873
0.8559	High Similarity	NPC139617
0.8548	High Similarity	NPC476343
0.8529	High Similarity	NPC209085
0.8529	High Similarity	NPC224884
0.8525	High Similarity	NPC70744
0.8525	High Similarity	NPC137537
0.8525	High Similarity	NPC164706
0.8525	High Similarity	NPC255675
0.8525	High Similarity	NPC272471
0.8525	High Similarity	NPC107588
0.8519	High Similarity	NPC472332
0.8519	High Similarity	NPC472335
0.8512	High Similarity	NPC221049
0.8504	High Similarity	NPC213552
0.8504	High Similarity	NPC120225
0.8485	Intermediate Similarity	NPC139519
0.8475	Intermediate Similarity	NPC137685
0.8473	Intermediate Similarity	NPC307006
0.8473	Intermediate Similarity	NPC129889
0.8468	Intermediate Similarity	NPC204466
0.8456	Intermediate Similarity	NPC141817
0.8456	Intermediate Similarity	NPC229218
0.8456	Intermediate Similarity	NPC169214
0.8456	Intermediate Similarity	NPC192597
0.8456	Intermediate Similarity	NPC176030
0.8455	Intermediate Similarity	NPC320987
0.8455	Intermediate Similarity	NPC181969
0.8444	Intermediate Similarity	NPC100675
0.8444	Intermediate Similarity	NPC29599
0.8444	Intermediate Similarity	NPC78987
0.8444	Intermediate Similarity	NPC82336
0.8444	Intermediate Similarity	NPC282291
0.8444	Intermediate Similarity	NPC166137
0.8443	Intermediate Similarity	NPC86947
0.8443	Intermediate Similarity	NPC185738
0.8443	Intermediate Similarity	NPC39793
0.8443	Intermediate Similarity	NPC280001
0.8438	Intermediate Similarity	NPC203719
0.8438	Intermediate Similarity	NPC117237
0.8425	Intermediate Similarity	NPC116907
0.8425	Intermediate Similarity	NPC228771
0.8425	Intermediate Similarity	NPC193544
0.8425	Intermediate Similarity	NPC221077
0.8425	Intermediate Similarity	NPC298757
0.8425	Intermediate Similarity	NPC17943
0.8425	Intermediate Similarity	NPC472093
0.8425	Intermediate Similarity	NPC289459
0.8425	Intermediate Similarity	NPC266705
0.8425	Intermediate Similarity	NPC57490
0.8425	Intermediate Similarity	NPC148627
0.8425	Intermediate Similarity	NPC475169
0.8425	Intermediate Similarity	NPC208950
0.8425	Intermediate Similarity	NPC203133
0.8425	Intermediate Similarity	NPC233410
0.8425	Intermediate Similarity	NPC173608
0.8425	Intermediate Similarity	NPC9067
0.8425	Intermediate Similarity	NPC251855
0.8425	Intermediate Similarity	NPC117214
0.8425	Intermediate Similarity	NPC29008
0.8413	Intermediate Similarity	NPC474691
0.8413	Intermediate Similarity	NPC197757
0.8413	Intermediate Similarity	NPC228922
0.84	Intermediate Similarity	NPC470804
0.84	Intermediate Similarity	NPC290451
0.84	Intermediate Similarity	NPC70752

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 NPC163083 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	270
0.1-0.2	934
0.2-0.3	1560
0.3-0.4	2650
0.4-0.5	1823
0.5-0.6	1104
0.6-0.7	684
0.7-0.8	119
0.8-0.85	4
0.85-0.9	2
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.9016	High Similarity	NPD4379	Clinical (unspecified phase)
0.8879	High Similarity	NPD228	Approved
0.8443	Intermediate Similarity	NPD5536	Phase 2
0.8438	Intermediate Similarity	NPD9494	Approved
0.8264	Intermediate Similarity	NPD5283	Phase 1
0.8168	Intermediate Similarity	NPD3027	Phase 3
0.7934	Intermediate Similarity	NPD3022	Approved
0.7934	Intermediate Similarity	NPD3021	Approved
0.7874	Intermediate Similarity	NPD1651	Approved
0.7857	Intermediate Similarity	NPD4109	Clinical (unspecified phase)
0.7857	Intermediate Similarity	NPD4110	Phase 3
0.7851	Intermediate Similarity	NPD2684	Approved
0.7817	Intermediate Similarity	NPD6143	Clinical (unspecified phase)
0.7778	Intermediate Similarity	NPD2674	Phase 3
0.7755	Intermediate Similarity	NPD1934	Approved
0.7742	Intermediate Similarity	NPD7843	Approved
0.7734	Intermediate Similarity	NPD1357	Approved
0.7721	Intermediate Similarity	NPD3619	Clinical (unspecified phase)
0.7721	Intermediate Similarity	NPD3620	Phase 2
0.7704	Intermediate Similarity	NPD6798	Discontinued
0.7703	Intermediate Similarity	NPD2801	Approved
0.7698	Intermediate Similarity	NPD7157	Approved
0.7664	Intermediate Similarity	NPD6355	Discontinued
0.7652	Intermediate Similarity	NPD1283	Approved
0.763	Intermediate Similarity	NPD7095	Approved
0.7615	Intermediate Similarity	NPD3847	Discontinued
0.7606	Intermediate Similarity	NPD8166	Discontinued
0.76	Intermediate Similarity	NPD3882	Suspended
0.7591	Intermediate Similarity	NPD825	Approved
0.7591	Intermediate Similarity	NPD4060	Phase 1
0.7591	Intermediate Similarity	NPD826	Approved
0.7586	Intermediate Similarity	NPD9296	Approved
0.7584	Intermediate Similarity	NPD2393	Clinical (unspecified phase)
0.7574	Intermediate Similarity	NPD3145	Approved
0.7574	Intermediate Similarity	NPD3144	Approved
0.7571	Intermediate Similarity	NPD2935	Discontinued
0.7556	Intermediate Similarity	NPD1529	Clinical (unspecified phase)
0.754	Intermediate Similarity	NPD1241	Discontinued
0.7538	Intermediate Similarity	NPD4626	Approved
0.7537	Intermediate Similarity	NPD258	Approved
0.7537	Intermediate Similarity	NPD257	Approved
0.7536	Intermediate Similarity	NPD447	Suspended
0.7518	Intermediate Similarity	NPD4062	Phase 3
0.7518	Intermediate Similarity	NPD6233	Phase 2
0.75	Intermediate Similarity	NPD3972	Approved
0.75	Intermediate Similarity	NPD7028	Phase 2
0.7481	Intermediate Similarity	NPD1530	Clinical (unspecified phase)
0.7464	Intermediate Similarity	NPD1612	Clinical (unspecified phase)
0.7464	Intermediate Similarity	NPD1613	Approved
0.7448	Intermediate Similarity	NPD1511	Approved
0.7444	Intermediate Similarity	NPD3600	Clinical (unspecified phase)
0.7424	Intermediate Similarity	NPD1535	Discovery
0.7424	Intermediate Similarity	NPD3705	Approved
0.7424	Intermediate Similarity	NPD1281	Approved
0.7422	Intermediate Similarity	NPD6671	Approved
0.741	Intermediate Similarity	NPD230	Phase 1
0.7407	Intermediate Similarity	NPD5647	Approved
0.7405	Intermediate Similarity	NPD3019	Approved
0.7405	Intermediate Similarity	NPD2932	Approved
0.7391	Intermediate Similarity	NPD259	Phase 1
0.7388	Intermediate Similarity	NPD1876	Approved
0.7386	Intermediate Similarity	NPD6234	Discontinued
0.7385	Intermediate Similarity	NPD1894	Discontinued
0.7372	Intermediate Similarity	NPD6167	Clinical (unspecified phase)
0.7372	Intermediate Similarity	NPD6166	Phase 2
0.7372	Intermediate Similarity	NPD6168	Clinical (unspecified phase)
0.7368	Intermediate Similarity	NPD1481	Phase 2
0.7368	Intermediate Similarity	NPD1608	Approved
0.7361	Intermediate Similarity	NPD4628	Phase 3
0.7357	Intermediate Similarity	NPD6653	Approved
0.7347	Intermediate Similarity	NPD1512	Approved
0.7339	Intermediate Similarity	NPD1358	Approved
0.7338	Intermediate Similarity	NPD1558	Phase 1
0.7315	Intermediate Similarity	NPD824	Approved
0.7313	Intermediate Similarity	NPD2983	Phase 2
0.7313	Intermediate Similarity	NPD2982	Phase 2
0.7297	Intermediate Similarity	NPD6980	Clinical (unspecified phase)
0.7286	Intermediate Similarity	NPD555	Phase 2
0.7285	Intermediate Similarity	NPD37	Approved
0.7273	Intermediate Similarity	NPD1778	Approved
0.7255	Intermediate Similarity	NPD4868	Clinical (unspecified phase)
0.7239	Intermediate Similarity	NPD2981	Phase 2
0.7227	Intermediate Similarity	NPD2859	Approved
0.7227	Intermediate Similarity	NPD2860	Approved
0.7226	Intermediate Similarity	NPD3018	Phase 2
0.7226	Intermediate Similarity	NPD9569	Approved
0.7222	Intermediate Similarity	NPD4534	Discontinued
0.7218	Intermediate Similarity	NPD3496	Discontinued
0.7214	Intermediate Similarity	NPD2979	Phase 3
0.7214	Intermediate Similarity	NPD1240	Approved
0.7214	Intermediate Similarity	NPD943	Approved
0.7206	Intermediate Similarity	NPD2797	Approved
0.7203	Intermediate Similarity	NPD2438	Suspended
0.72	Intermediate Similarity	NPD3455	Phase 2
0.72	Intermediate Similarity	NPD290	Approved
0.7197	Intermediate Similarity	NPD5691	Approved
0.7194	Intermediate Similarity	NPD6859	Clinical (unspecified phase)
0.7194	Intermediate Similarity	NPD5111	Phase 2
0.7194	Intermediate Similarity	NPD5110	Phase 2
0.7194	Intermediate Similarity	NPD3268	Approved
0.7194	Intermediate Similarity	NPD5109	Approved
0.7192	Intermediate Similarity	NPD6190	Approved
0.719	Intermediate Similarity	NPD3817	Phase 2
0.719	Intermediate Similarity	NPD3020	Approved
0.7188	Intermediate Similarity	NPD5535	Approved
0.7188	Intermediate Similarity	NPD7074	Phase 3
0.7174	Intermediate Similarity	NPD2614	Approved
0.7172	Intermediate Similarity	NPD3060	Approved
0.717	Intermediate Similarity	NPD3818	Discontinued
0.7163	Intermediate Similarity	NPD275	Approved
0.7163	Intermediate Similarity	NPD274	Approved
0.7162	Intermediate Similarity	NPD3146	Approved
0.7162	Intermediate Similarity	NPD3688	Clinical (unspecified phase)
0.7153	Intermediate Similarity	NPD2798	Approved
0.7153	Intermediate Similarity	NPD2344	Approved
0.7153	Intermediate Similarity	NPD6584	Phase 3
0.7143	Intermediate Similarity	NPD17	Approved
0.7143	Intermediate Similarity	NPD4966	Approved
0.7143	Intermediate Similarity	NPD2933	Approved
0.7143	Intermediate Similarity	NPD2934	Approved
0.7143	Intermediate Similarity	NPD4967	Phase 2
0.7143	Intermediate Similarity	NPD1432	Clinical (unspecified phase)
0.7143	Intermediate Similarity	NPD1726	Clinical (unspecified phase)
0.7143	Intermediate Similarity	NPD4965	Approved
0.7143	Intermediate Similarity	NPD8032	Phase 2
0.7134	Intermediate Similarity	NPD6232	Discontinued
0.7133	Intermediate Similarity	NPD2799	Discontinued
0.7133	Intermediate Similarity	NPD1510	Phase 2
0.7125	Intermediate Similarity	NPD7054	Approved
0.7121	Intermediate Similarity	NPD9545	Approved
0.712	Intermediate Similarity	NPD3134	Approved
0.7113	Intermediate Similarity	NPD1607	Approved
0.7113	Intermediate Similarity	NPD2653	Approved
0.7107	Intermediate Similarity	NPD7473	Discontinued
0.7103	Intermediate Similarity	NPD5958	Discontinued
0.7103	Intermediate Similarity	NPD2424	Discontinued
0.7095	Intermediate Similarity	NPD4357	Discontinued
0.7087	Intermediate Similarity	NPD5451	Approved
0.7086	Intermediate Similarity	NPD3866	Clinical (unspecified phase)
0.7083	Intermediate Similarity	NPD844	Approved
0.7083	Intermediate Similarity	NPD6099	Approved
0.7083	Intermediate Similarity	NPD2239	Approved
0.7083	Intermediate Similarity	NPD6100	Approved
0.7083	Intermediate Similarity	NPD2240	Approved
0.7083	Intermediate Similarity	NPD2161	Phase 2
0.7081	Intermediate Similarity	NPD7472	Approved
0.708	Intermediate Similarity	NPD987	Approved
0.7073	Intermediate Similarity	NPD291	Approved
0.707	Intermediate Similarity	NPD7199	Phase 2
0.7068	Intermediate Similarity	NPD5585	Approved
0.7067	Intermediate Similarity	NPD3639	Approved
0.7067	Intermediate Similarity	NPD6662	Clinical (unspecified phase)
0.7067	Intermediate Similarity	NPD3641	Approved
0.7067	Intermediate Similarity	NPD3640	Phase 3
0.7063	Intermediate Similarity	NPD7228	Approved
0.7055	Intermediate Similarity	NPD7421	Clinical (unspecified phase)
0.7054	Intermediate Similarity	NPD9379	Approved
0.7054	Intermediate Similarity	NPD821	Approved
0.7054	Intermediate Similarity	NPD9377	Approved
0.705	Intermediate Similarity	NPD5752	Clinical (unspecified phase)
0.7047	Intermediate Similarity	NPD4378	Clinical (unspecified phase)
0.7039	Intermediate Similarity	NPD4380	Phase 2
0.7034	Intermediate Similarity	NPD7266	Discontinued
0.702	Intermediate Similarity	NPD3686	Approved
0.702	Intermediate Similarity	NPD3687	Approved
0.7015	Intermediate Similarity	NPD6516	Phase 2
0.7015	Intermediate Similarity	NPD2667	Approved
0.7015	Intermediate Similarity	NPD2668	Approved
0.7015	Intermediate Similarity	NPD5846	Approved
0.7012	Intermediate Similarity	NPD3534	Clinical (unspecified phase)
0.7007	Intermediate Similarity	NPD196	Phase 1
0.7007	Intermediate Similarity	NPD2922	Phase 1
0.7	Intermediate Similarity	NPD9537	Phase 1
0.7	Intermediate Similarity	NPD9536	Phase 1
0.6993	Remote Similarity	NPD6873	Phase 2
0.6986	Remote Similarity	NPD970	Clinical (unspecified phase)
0.6985	Remote Similarity	NPD9717	Approved
0.6985	Remote Similarity	NPD2232	Approved
0.6985	Remote Similarity	NPD9269	Phase 2
0.6985	Remote Similarity	NPD2233	Approved
0.6985	Remote Similarity	NPD2230	Approved
0.6984	Remote Similarity	NPD968	Approved
0.6981	Remote Similarity	NPD7184	Clinical (unspecified phase)
0.6978	Remote Similarity	NPD2861	Phase 2
0.6974	Remote Similarity	NPD7458	Discontinued
0.6974	Remote Similarity	NPD3111	Phase 1
0.697	Remote Similarity	NPD9493	Approved
0.6966	Remote Similarity	NPD4477	Approved
0.6966	Remote Similarity	NPD6032	Approved
0.6966	Remote Similarity	NPD2531	Phase 2
0.6966	Remote Similarity	NPD4476	Approved
0.6963	Remote Similarity	NPD3023	Approved
0.6963	Remote Similarity	NPD3026	Approved
0.6962	Remote Similarity	NPD8127	Discontinued
0.6959	Remote Similarity	NPD2309	Approved
0.6959	Remote Similarity	NPD2219	Phase 1
0.6959	Remote Similarity	NPD2354	Approved
0.695	Remote Similarity	NPD5718	Phase 2
0.6947	Remote Similarity	NPD690	Clinical (unspecified phase)
0.6944	Remote Similarity	NPD6896	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