NPASS Compound

Structure

CID41333 OpenBabel06191715372D 24 24 0 0 1 0 0 0 0 0999 V2000 -8.4964 2.4168 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -10.0787 1.7123 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.8749 -1.3420 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7103 0.0670 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.6829 0.5897 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.6993 0.2761 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.6774 0.6942 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.2761 -0.3239 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.6938 0.3806 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2926 -0.6375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8968 -1.7601 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6180 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3090 -0.9511 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.0841 1.6077 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.2816 -0.4284 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2981 -0.7420 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3090 -0.9511 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8913 -1.6555 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8090 0.5878 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -0.8090 1.5878 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -3.4791 -2.4646 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.6750 2.0878 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0570 2.0878 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 14 1 0 0 0 0 2 14 1 0 0 0 0 3 15 1 0 0 0 0 4 16 1 0 0 0 0 5 7 1 0 0 0 0 5 8 1 0 0 0 0 6 9 1 0 0 0 0 6 10 1 0 0 0 0 7 14 2 0 0 0 0 8 15 1 0 0 0 0 9 15 2 0 0 0 0 10 16 2 0 0 0 0 11 17 1 0 0 0 0 11 18 1 0 0 0 0 12 17 1 0 0 0 0 12 19 2 0 0 0 0 13 17 2 0 0 0 0 13 20 1 0 0 0 0 16 18 1 0 0 0 0 18 22 1 1 0 0 0 19 20 1 0 0 0 0 19 21 1 0 0 0 0 21 23 2 0 0 0 0 21 24 2 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	332.21
Volume:	361.169
LogP:	4.222
LogD:	4.199
LogS:	-4.763
# Rotatable Bonds:	9
TPSA:	79.16
# H-Bond Aceptor:	5
# H-Bond Donor:	2
# Rings:	1
# Heavy Atoms:	5

MedChem Properties

QED Drug-Likeness Score:	0.385
Synthetic Accessibility Score:	4.049
Fsp3:	0.474
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.556
MDCK Permeability:	1.0311862752132583e-05
Pgp-inhibitor:	0.215
Pgp-substrate:	0.784
Human Intestinal Absorption (HIA):	0.087
20% Bioavailability (F20%):	0.018
30% Bioavailability (F30%):	0.01

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.578
Plasma Protein Binding (PPB):	98.37940216064453%
Volume Distribution (VD):	1.196
Pgp-substrate:	1.6700828075408936%

ADMET: Metabolism

CYP1A2-inhibitor:	0.754
CYP1A2-substrate:	0.517
CYP2C19-inhibitor:	0.953
CYP2C19-substrate:	0.161
CYP2C9-inhibitor:	0.794
CYP2C9-substrate:	0.979
CYP2D6-inhibitor:	0.829
CYP2D6-substrate:	0.863
CYP3A4-inhibitor:	0.617
CYP3A4-substrate:	0.185

ADMET: Excretion

Clearance (CL):	7.49
Half-life (T1/2):	0.388

ADMET: Toxicity

hERG Blockers:	0.157
Human Hepatotoxicity (H-HT):	0.909
Drug-inuced Liver Injury (DILI):	0.042
AMES Toxicity:	0.096
Rat Oral Acute Toxicity:	0.07
Maximum Recommended Daily Dose:	0.985
Skin Sensitization:	0.961
Carcinogencity:	0.045
Eye Corrosion:	0.037
Eye Irritation:	0.806
Respiratory Toxicity:	0.953

Download Data

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

Natural Product: NPC41333

Natural Product ID:	NPC41333
*Common Name:**	Nitropyrrolin D
IUPAC Name:	(2R,3E,6E)-3,7,11-trimethyl-1-(5-nitro-1H-pyrrol-3-yl)dodeca-3,6,10-trien-2-ol
Synonyms:	Nitropyrrolin D
Standard InCHIKey:	COVDAEBDAVGGFK-CIBVNXTLSA-N
Standard InCHI:	InChI=1S/C19H28N2O3/c1-14(2)7-5-8-15(3)9-6-10-16(4)18(22)11-17-12-19(20-13-17)21(23)24/h7,9-10,12-13,18,20,22H,5-6,8,11H2,1-4H3/b15-9+,16-10+/t18-/m1/s1
SMILES:	CC(=CCC/C(=C/C/C=C(C)/[C@@H](Cc1cc([nH]c1)N(=O)=O)O)/C)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL1651437
PubChem CID:	50908454
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001550] Sesquiterpenoids

*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
NPO30294	Streptomyces sp. cnq-509	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	PMID[21090803]
NPO33614	actinomycete sp. CNQ-509	Species	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[21090803]

☑ 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	1
MIC	1

Activity Type	# Activity
Cell Line	1
Organism	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT393	Cell Line	HCT-116	Homo sapiens	IC50	=	5700.0	nM	PMID[486233]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	>	20.0	ug.mL-1	PMID[486233]

☑ 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 NPC41333 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	288
0.1-0.2	5059
0.2-0.3	26346
0.3-0.4	5784
0.4-0.5	3004
0.5-0.6	1928
0.6-0.7	281
0.7-0.8	2
0.8-0.85	0
0.85-0.9	2
0.9-0.95	2
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
0.9363	High Similarity	NPC89562
0.9304	High Similarity	NPC313730
0.9051	High Similarity	NPC34300
0.9018	High Similarity	NPC314491
0.7086	Intermediate Similarity	NPC162268
0.7052	Intermediate Similarity	NPC212742
0.6989	Remote Similarity	NPC311276
0.6933	Remote Similarity	NPC62151
0.6914	Remote Similarity	NPC230869
0.6893	Remote Similarity	NPC102423
0.6893	Remote Similarity	NPC40779
0.6882	Remote Similarity	NPC163421
0.6882	Remote Similarity	NPC188387
0.6871	Remote Similarity	NPC314646
0.6857	Remote Similarity	NPC469762
0.6851	Remote Similarity	NPC313791
0.68	Remote Similarity	NPC469785
0.678	Remote Similarity	NPC131718
0.6763	Remote Similarity	NPC105818
0.6763	Remote Similarity	NPC24678
0.6686	Remote Similarity	NPC469760
0.6686	Remote Similarity	NPC25008
0.6686	Remote Similarity	NPC73952
0.6686	Remote Similarity	NPC259644
0.6686	Remote Similarity	NPC469763
0.6686	Remote Similarity	NPC469765
0.6686	Remote Similarity	NPC469786
0.6667	Remote Similarity	NPC138018
0.6648	Remote Similarity	NPC211572
0.6648	Remote Similarity	NPC75540
0.6648	Remote Similarity	NPC80597
0.6648	Remote Similarity	NPC212376
0.6648	Remote Similarity	NPC70922
0.663	Remote Similarity	NPC160105
0.663	Remote Similarity	NPC49217
0.663	Remote Similarity	NPC54988
0.663	Remote Similarity	NPC49954
0.663	Remote Similarity	NPC474561
0.6628	Remote Similarity	NPC159856
0.6628	Remote Similarity	NPC314372
0.6626	Remote Similarity	NPC89490
0.6614	Remote Similarity	NPC314002
0.6612	Remote Similarity	NPC470498
0.6611	Remote Similarity	NPC469813
0.6611	Remote Similarity	NPC476446
0.6611	Remote Similarity	NPC78375
0.6597	Remote Similarity	NPC32771
0.6596	Remote Similarity	NPC469358
0.6585	Remote Similarity	NPC329896
0.6585	Remote Similarity	NPC475105
0.6585	Remote Similarity	NPC475090
0.658	Remote Similarity	NPC304187
0.658	Remote Similarity	NPC477166
0.6579	Remote Similarity	NPC171171
0.657	Remote Similarity	NPC471323
0.6564	Remote Similarity	NPC165370
0.6564	Remote Similarity	NPC306397
0.6564	Remote Similarity	NPC212125
0.6562	Remote Similarity	NPC95783
0.6561	Remote Similarity	NPC204717
0.6559	Remote Similarity	NPC151939
0.6556	Remote Similarity	NPC282231
0.6556	Remote Similarity	NPC71079
0.6554	Remote Similarity	NPC477815
0.6543	Remote Similarity	NPC71037
0.6543	Remote Similarity	NPC233936
0.6524	Remote Similarity	NPC141377
0.6519	Remote Similarity	NPC474217
0.6515	Remote Similarity	NPC470497
0.6512	Remote Similarity	NPC190296
0.651	Remote Similarity	NPC209917
0.6508	Remote Similarity	NPC220765
0.6508	Remote Similarity	NPC163055
0.6506	Remote Similarity	NPC471322
0.6503	Remote Similarity	NPC63751
0.6503	Remote Similarity	NPC201700
0.65	Remote Similarity	NPC279918
0.6497	Remote Similarity	NPC470499
0.6495	Remote Similarity	NPC99666
0.6492	Remote Similarity	NPC315555
0.6486	Remote Similarity	NPC314603
0.6484	Remote Similarity	NPC85918
0.648	Remote Similarity	NPC242209
0.6471	Remote Similarity	NPC184964
0.6462	Remote Similarity	NPC474177
0.6458	Remote Similarity	NPC46580
0.6448	Remote Similarity	NPC278366
0.6448	Remote Similarity	NPC127730
0.6446	Remote Similarity	NPC327941
0.6444	Remote Similarity	NPC92796
0.6444	Remote Similarity	NPC135141
0.6436	Remote Similarity	NPC215795
0.6436	Remote Similarity	NPC176199
0.6429	Remote Similarity	NPC133366
0.6429	Remote Similarity	NPC194640
0.642	Remote Similarity	NPC282531
0.6413	Remote Similarity	NPC319456
0.6408	Remote Similarity	NPC471603
0.6402	Remote Similarity	NPC300688
0.6398	Remote Similarity	NPC34508
0.6396	Remote Similarity	NPC251090
0.6389	Remote Similarity	NPC475870
0.6383	Remote Similarity	NPC96890
0.6383	Remote Similarity	NPC68354
0.6383	Remote Similarity	NPC248454
0.6378	Remote Similarity	NPC267343
0.6378	Remote Similarity	NPC307963
0.6377	Remote Similarity	NPC282247
0.6374	Remote Similarity	NPC104049
0.6373	Remote Similarity	NPC317030
0.6364	Remote Similarity	NPC37423
0.6364	Remote Similarity	NPC275305
0.6364	Remote Similarity	NPC471313
0.6364	Remote Similarity	NPC471311
0.6359	Remote Similarity	NPC320968
0.6353	Remote Similarity	NPC29702
0.6349	Remote Similarity	NPC472443
0.6338	Remote Similarity	NPC130570
0.6337	Remote Similarity	NPC98715
0.6335	Remote Similarity	NPC48938
0.6327	Remote Similarity	NPC473342
0.6327	Remote Similarity	NPC477167
0.6321	Remote Similarity	NPC473317
0.6321	Remote Similarity	NPC474707
0.6319	Remote Similarity	NPC290094
0.6318	Remote Similarity	NPC300183
0.6308	Remote Similarity	NPC154339
0.6301	Remote Similarity	NPC469779
0.6301	Remote Similarity	NPC469784
0.6301	Remote Similarity	NPC469780
0.6301	Remote Similarity	NPC469767
0.6301	Remote Similarity	NPC469761
0.6301	Remote Similarity	NPC469768
0.6301	Remote Similarity	NPC469783
0.6296	Remote Similarity	NPC111275
0.6296	Remote Similarity	NPC59269
0.6289	Remote Similarity	NPC204565
0.6281	Remote Similarity	NPC77555
0.6281	Remote Similarity	NPC156704
0.628	Remote Similarity	NPC27740
0.6278	Remote Similarity	NPC470507
0.6271	Remote Similarity	NPC471957
0.6269	Remote Similarity	NPC15102
0.6269	Remote Similarity	NPC280290
0.6264	Remote Similarity	NPC469766
0.6263	Remote Similarity	NPC270009
0.6256	Remote Similarity	NPC65215
0.6256	Remote Similarity	NPC173028
0.625	Remote Similarity	NPC476118
0.625	Remote Similarity	NPC472444
0.6244	Remote Similarity	NPC46225
0.6244	Remote Similarity	NPC225821
0.6243	Remote Similarity	NPC73767
0.6243	Remote Similarity	NPC267885
0.6237	Remote Similarity	NPC235684
0.6237	Remote Similarity	NPC78020
0.6237	Remote Similarity	NPC317430
0.6233	Remote Similarity	NPC125597
0.6232	Remote Similarity	NPC5145
0.623	Remote Similarity	NPC63338
0.623	Remote Similarity	NPC322976
0.623	Remote Similarity	NPC324203
0.6224	Remote Similarity	NPC76748
0.6221	Remote Similarity	NPC84911
0.6218	Remote Similarity	NPC165495
0.6215	Remote Similarity	NPC143872
0.6214	Remote Similarity	NPC314957
0.6214	Remote Similarity	NPC127677
0.6214	Remote Similarity	NPC476465
0.6214	Remote Similarity	NPC258062
0.6213	Remote Similarity	NPC324611
0.6213	Remote Similarity	NPC256893
0.6212	Remote Similarity	NPC106937
0.6211	Remote Similarity	NPC293472
0.6207	Remote Similarity	NPC193761
0.6207	Remote Similarity	NPC476874
0.6205	Remote Similarity	NPC202957
0.6205	Remote Similarity	NPC169625
0.6203	Remote Similarity	NPC194411
0.6198	Remote Similarity	NPC192270
0.6195	Remote Similarity	NPC475288
0.6193	Remote Similarity	NPC92111
0.619	Remote Similarity	NPC203468
0.619	Remote Similarity	NPC149155
0.619	Remote Similarity	NPC110500
0.6183	Remote Similarity	NPC125659
0.6183	Remote Similarity	NPC168702
0.6178	Remote Similarity	NPC248041
0.6178	Remote Similarity	NPC126709
0.6173	Remote Similarity	NPC296527
0.6173	Remote Similarity	NPC472289
0.6172	Remote Similarity	NPC87856
0.6172	Remote Similarity	NPC151976
0.6169	Remote Similarity	NPC131887
0.6165	Remote Similarity	NPC88008
0.6163	Remote Similarity	NPC261195
0.6163	Remote Similarity	NPC96102
0.6163	Remote Similarity	NPC29886
0.6158	Remote Similarity	NPC475506
0.6154	Remote Similarity	NPC315320

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 NPC41333 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	153
0.1-0.2	726
0.2-0.3	1369
0.3-0.4	2650
0.4-0.5	2526
0.5-0.6	1579
0.6-0.7	146
0.7-0.8	1
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
0.7688	Intermediate Similarity	NPD2928	Phase 2
0.7112	Intermediate Similarity	NPD2127	Suspended
0.6964	Remote Similarity	NPD1352	Discontinued
0.6909	Remote Similarity	NPD9506	Approved
0.6869	Remote Similarity	NPD4612	Discontinued
0.6859	Remote Similarity	NPD4999	Phase 3
0.6859	Remote Similarity	NPD4998	Phase 3
0.6839	Remote Similarity	NPD5358	Clinical (unspecified phase)
0.6818	Remote Similarity	NPD8410	Clinical (unspecified phase)
0.68	Remote Similarity	NPD3014	Clinical (unspecified phase)
0.68	Remote Similarity	NPD3013	Phase 3
0.6778	Remote Similarity	NPD5069	Clinical (unspecified phase)
0.6742	Remote Similarity	NPD4239	Clinical (unspecified phase)
0.674	Remote Similarity	NPD2620	Phase 2
0.674	Remote Similarity	NPD4184	Clinical (unspecified phase)
0.674	Remote Similarity	NPD2619	Clinical (unspecified phase)
0.6724	Remote Similarity	NPD3262	Approved
0.6667	Remote Similarity	NPD2872	Phase 2
0.6648	Remote Similarity	NPD8026	Phase 1
0.6633	Remote Similarity	NPD4683	Phase 3
0.6633	Remote Similarity	NPD3814	Phase 1
0.6633	Remote Similarity	NPD1915	Phase 1
0.6618	Remote Similarity	NPD4555	Clinical (unspecified phase)
0.6614	Remote Similarity	NPD2814	Clinical (unspecified phase)
0.6608	Remote Similarity	NPD1427	Clinical (unspecified phase)
0.6606	Remote Similarity	NPD9726	Discontinued
0.6599	Remote Similarity	NPD2332	Discontinued
0.6579	Remote Similarity	NPD706	Phase 1
0.6578	Remote Similarity	NPD6595	Phase 3
0.6567	Remote Similarity	NPD4533	Clinical (unspecified phase)
0.6564	Remote Similarity	NPD9080	Approved
0.6564	Remote Similarity	NPD9284	Approved
0.6562	Remote Similarity	NPD2544	Clinical (unspecified phase)
0.6543	Remote Similarity	NPD3178	Discontinued
0.6541	Remote Similarity	NPD5065	Approved
0.6502	Remote Similarity	NPD6545	Clinical (unspecified phase)
0.6495	Remote Similarity	NPD1234	Discontinued
0.6474	Remote Similarity	NPD3813	Approved
0.6471	Remote Similarity	NPD8321	Discontinued
0.6443	Remote Similarity	NPD459	Clinical (unspecified phase)
0.6439	Remote Similarity	NPD4563	Phase 2
0.6436	Remote Similarity	NPD4076	Approved
0.6436	Remote Similarity	NPD4079	Approved
0.6435	Remote Similarity	NPD3960	Clinical (unspecified phase)
0.6425	Remote Similarity	NPD276	Clinical (unspecified phase)
0.641	Remote Similarity	NPD4615	Phase 2
0.6408	Remote Similarity	NPD3976	Clinical (unspecified phase)
0.6404	Remote Similarity	NPD2012	Clinical (unspecified phase)
0.6402	Remote Similarity	NPD2599	Approved
0.6402	Remote Similarity	NPD2601	Approved
0.6402	Remote Similarity	NPD2600	Approved
0.6398	Remote Similarity	NPD1599	Approved
0.6395	Remote Similarity	NPD1649	Discontinued
0.6392	Remote Similarity	NPD1043	Phase 3
0.6391	Remote Similarity	NPD2140	Approved
0.6391	Remote Similarity	NPD2142	Approved
0.6391	Remote Similarity	NPD2141	Approved
0.6384	Remote Similarity	NPD4463	Approved
0.6384	Remote Similarity	NPD4462	Approved
0.6383	Remote Similarity	NPD3506	Approved
0.6383	Remote Similarity	NPD3505	Approved
0.6378	Remote Similarity	NPD5575	Clinical (unspecified phase)
0.6378	Remote Similarity	NPD1038	Approved
0.6378	Remote Similarity	NPD1173	Approved
0.6374	Remote Similarity	NPD203	Clinical (unspecified phase)
0.6368	Remote Similarity	NPD1570	Approved
0.6368	Remote Similarity	NPD5486	Discontinued
0.6364	Remote Similarity	NPD2089	Clinical (unspecified phase)
0.6364	Remote Similarity	NPD2952	Discontinued
0.6359	Remote Similarity	NPD5611	Phase 2
0.6358	Remote Similarity	NPD1592	Phase 3
0.634	Remote Similarity	NPD2152	Clinical (unspecified phase)
0.6308	Remote Similarity	NPD5117	Phase 2
0.6296	Remote Similarity	NPD2144	Approved
0.6283	Remote Similarity	NPD1783	Clinical (unspecified phase)
0.6281	Remote Similarity	NPD7948	Phase 1
0.6275	Remote Similarity	NPD5458	Discontinued
0.6275	Remote Similarity	NPD4559	Clinical (unspecified phase)
0.6274	Remote Similarity	NPD245	Suspended
0.6271	Remote Similarity	NPD4702	Approved
0.6271	Remote Similarity	NPD4703	Approved
0.6269	Remote Similarity	NPD3082	Discontinued
0.6264	Remote Similarity	NPD1382	Phase 2
0.6264	Remote Similarity	NPD1383	Phase 3
0.6257	Remote Similarity	NPD3347	Clinical (unspecified phase)
0.625	Remote Similarity	NPD5596	Phase 2
0.625	Remote Similarity	NPD8458	Clinical (unspecified phase)
0.625	Remote Similarity	NPD2095	Phase 2
0.625	Remote Similarity	NPD5925	Phase 1
0.625	Remote Similarity	NPD5138	Approved
0.625	Remote Similarity	NPD3916	Clinical (unspecified phase)
0.625	Remote Similarity	NPD3918	Approved
0.625	Remote Similarity	NPD5140	Approved
0.625	Remote Similarity	NPD3917	Approved
0.625	Remote Similarity	NPD2094	Phase 2
0.625	Remote Similarity	NPD2092	Phase 2
0.6244	Remote Similarity	NPD1392	Approved
0.6244	Remote Similarity	NPD796	Phase 2
0.6243	Remote Similarity	NPD749	Clinical (unspecified phase)
0.6243	Remote Similarity	NPD786	Approved
0.6232	Remote Similarity	NPD7809	Clinical (unspecified phase)
0.623	Remote Similarity	NPD9398	Clinical (unspecified phase)
0.6229	Remote Similarity	NPD3717	Discontinued
0.6224	Remote Similarity	NPD3439	Approved
0.622	Remote Similarity	NPD8488	Clinical (unspecified phase)
0.6218	Remote Similarity	NPD1096	Discontinued
0.6218	Remote Similarity	NPD2091	Phase 2
0.6218	Remote Similarity	NPD2096	Phase 2
0.6214	Remote Similarity	NPD2187	Approved
0.6214	Remote Similarity	NPD2189	Approved
0.6212	Remote Similarity	NPD802	Phase 2
0.6212	Remote Similarity	NPD5428	Discontinued
0.6211	Remote Similarity	NPD6203	Clinical (unspecified phase)
0.6203	Remote Similarity	NPD1326	Approved
0.6203	Remote Similarity	NPD1325	Approved
0.6202	Remote Similarity	NPD3915	Approved
0.62	Remote Similarity	NPD3830	Phase 1
0.6198	Remote Similarity	NPD3038	Discontinued
0.6196	Remote Similarity	NPD2480	Clinical (unspecified phase)
0.6193	Remote Similarity	NPD4699	Discontinued
0.6193	Remote Similarity	NPD6022	Clinical (unspecified phase)
0.619	Remote Similarity	NPD482	Approved
0.6188	Remote Similarity	NPD2536	Discontinued
0.6185	Remote Similarity	NPD852	Discontinued
0.6184	Remote Similarity	NPD6529	Discontinued
0.6178	Remote Similarity	NPD2930	Clinical (unspecified phase)
0.6175	Remote Similarity	NPD5255	Approved
0.6175	Remote Similarity	NPD6165	Phase 2
0.6175	Remote Similarity	NPD6164	Phase 2
0.6173	Remote Similarity	NPD4021	Phase 2
0.617	Remote Similarity	NPD1567	Clinical (unspecified phase)
0.617	Remote Similarity	NPD2993	Clinical (unspecified phase)
0.6163	Remote Similarity	NPD198	Clinical (unspecified phase)
0.6162	Remote Similarity	NPD3406	Suspended
0.6162	Remote Similarity	NPD6887	Clinical (unspecified phase)
0.6158	Remote Similarity	NPD8629	Discontinued
0.6154	Remote Similarity	NPD9207	Approved
0.6154	Remote Similarity	NPD9206	Approved
0.6154	Remote Similarity	NPD6026	Approved
0.615	Remote Similarity	NPD534	Phase 2
0.615	Remote Similarity	NPD537	Phase 2
0.6146	Remote Similarity	NPD944	Approved
0.6141	Remote Similarity	NPD687	Clinical (unspecified phase)
0.6139	Remote Similarity	NPD5828	Phase 2
0.6135	Remote Similarity	NPD7947	Clinical (unspecified phase)
0.6131	Remote Similarity	NPD3485	Clinical (unspecified phase)
0.6131	Remote Similarity	NPD1304	Clinical (unspecified phase)
0.6126	Remote Similarity	NPD2293	Phase 2
0.6125	Remote Similarity	NPD269	Clinical (unspecified phase)
0.6124	Remote Similarity	NPD949	Phase 1
0.6122	Remote Similarity	NPD3002	Clinical (unspecified phase)
0.6122	Remote Similarity	NPD8431	Approved
0.6117	Remote Similarity	NPD6403	Clinical (unspecified phase)
0.6114	Remote Similarity	NPD4891	Phase 2
0.6114	Remote Similarity	NPD1395	Clinical (unspecified phase)
0.6114	Remote Similarity	NPD4649	Clinical (unspecified phase)
0.6109	Remote Similarity	NPD7415	Suspended
0.6108	Remote Similarity	NPD484	Approved
0.6105	Remote Similarity	NPD4128	Approved
0.6103	Remote Similarity	NPD2724	Phase 1
0.6103	Remote Similarity	NPD6610	Clinical (unspecified phase)
0.6099	Remote Similarity	NPD3405	Phase 3
0.6096	Remote Similarity	NPD4213	Clinical (unspecified phase)
0.6093	Remote Similarity	NPD4187	Clinical (unspecified phase)
0.6092	Remote Similarity	NPD1380	Discovery
0.6091	Remote Similarity	NPD6363	Clinical (unspecified phase)
0.6091	Remote Similarity	NPD8110	Clinical (unspecified phase)
0.6089	Remote Similarity	NPD1982	Phase 1
0.6087	Remote Similarity	NPD6135	Phase 1
0.6083	Remote Similarity	NPD7269	Clinical (unspecified phase)
0.608	Remote Similarity	NPD1722	Approved
0.6078	Remote Similarity	NPD3911	Approved
0.6073	Remote Similarity	NPD2367	Phase 2
0.6071	Remote Similarity	NPD1598	Discontinued
0.607	Remote Similarity	NPD2482	Clinical (unspecified phase)
0.6064	Remote Similarity	NPD2844	Phase 3
0.6061	Remote Similarity	NPD3870	Clinical (unspecified phase)
0.6061	Remote Similarity	NPD3871	Clinical (unspecified phase)
0.6056	Remote Similarity	NPD7980	Clinical (unspecified phase)
0.6056	Remote Similarity	NPD3100	Discontinued
0.6054	Remote Similarity	NPD2511	Approved
0.6053	Remote Similarity	NPD3224	Phase 2
0.605	Remote Similarity	NPD460	Discontinued
0.6048	Remote Similarity	NPD3570	Phase 2
0.6045	Remote Similarity	NPD2007	Clinical (unspecified phase)
0.6043	Remote Similarity	NPD1002	Clinical (unspecified phase)
0.6042	Remote Similarity	NPD4072	Approved
0.6042	Remote Similarity	NPD4181	Approved
0.6042	Remote Similarity	NPD5751	Clinical (unspecified phase)
0.6042	Remote Similarity	NPD4071	Approved
0.604	Remote Similarity	NPD1622	Discontinued
0.6039	Remote Similarity	NPD4862	Clinical (unspecified phase)
0.6037	Remote Similarity	NPD7202	Clinical (unspecified phase)
0.6034	Remote Similarity	NPD1363	Phase 3
0.6034	Remote Similarity	NPD6148	Clinical (unspecified phase)
0.603	Remote Similarity	NPD4148	Approved
0.6029	Remote Similarity	NPD2911	Approved
0.6029	Remote Similarity	NPD2912	Approved
0.6022	Remote Similarity	NPD2172	Phase 1
0.6022	Remote Similarity	NPD418	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