NPASS Compound

Structure

Physi-Chem Properties

Molecular Weight:	273.11
Volume:	268.573
LogP:	0.561
LogD:	0.499
LogS:	-2.013
# Rotatable Bonds:	3
TPSA:	94.22
# H-Bond Aceptor:	6
# H-Bond Donor:	4
# Rings:	3
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.617
Synthetic Accessibility Score:	3.04
Fsp3:	0.286
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.952
MDCK Permeability:	4.52255699201487e-06
Pgp-inhibitor:	0.0
Pgp-substrate:	0.008
Human Intestinal Absorption (HIA):	0.903
20% Bioavailability (F20%):	0.891
30% Bioavailability (F30%):	0.949

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.841
Plasma Protein Binding (PPB):	17.739397048950195%
Volume Distribution (VD):	0.463
Pgp-substrate:	73.95520782470703%

ADMET: Metabolism

CYP1A2-inhibitor:	0.045
CYP1A2-substrate:	0.093
CYP2C19-inhibitor:	0.076
CYP2C19-substrate:	0.061
CYP2C9-inhibitor:	0.054
CYP2C9-substrate:	0.752
CYP2D6-inhibitor:	0.007
CYP2D6-substrate:	0.366
CYP3A4-inhibitor:	0.07
CYP3A4-substrate:	0.08

ADMET: Excretion

Clearance (CL):	3.374
Half-life (T1/2):	0.792

ADMET: Toxicity

hERG Blockers:	0.031
Human Hepatotoxicity (H-HT):	0.144
Drug-inuced Liver Injury (DILI):	0.153
AMES Toxicity:	0.244
Rat Oral Acute Toxicity:	0.689
Maximum Recommended Daily Dose:	0.069
Skin Sensitization:	0.156
Carcinogencity:	0.101
Eye Corrosion:	0.003
Eye Irritation:	0.012
Respiratory Toxicity:	0.059

Download Data

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

Natural Product: NPC54988

Natural Product ID:	NPC54988
*Common Name:**	(3S,6S)-3-(Hydroxymethyl)-6-(1H-Indol-3-Ylmethyl)Piperazine-2,5-Dione
IUPAC Name:	(3S,6S)-3-(hydroxymethyl)-6-(1H-indol-3-ylmethyl)piperazine-2,5-dione
Synonyms:
Standard InCHIKey:	GNBUEEFSNREBQN-RYUDHWBXSA-N
Standard InCHI:	InChI=1S/C14H15N3O3/c18-7-12-14(20)16-11(13(19)17-12)5-8-6-15-10-4-2-1-3-9(8)10/h1-4,6,11-12,15,18H,5,7H2,(H,16,20)(H,17,19)/t11-,12-/m0/s1
SMILES:	OC[C@@H]1N=C(O)[C@@H](N=C1O)Cc1c[nH]c2c1cccc2
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL2047546
PubChem CID:	70694585
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000264] Organic acids and derivatives [CHEMONTID:0000265] Carboxylic acids and derivatives [CHEMONTID:0000013] Amino acids, peptides, and analogues [CHEMONTID:0000347] Amino acids and derivatives [CHEMONTID:0000060] Alpha amino acids and derivatives

*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
NPO5778	Oidiodendron truncatum	Species	Myxotrichaceae	Eukaryota	n.a.	Antarctic	n.a.	PMID[22583079]
NPO32990	acrostalagmus luteoalbus scsio f457	Species	Plectosphaerellaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23079524]
NPO5778	Oidiodendron truncatum	Species	Myxotrichaceae	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	9

Activity Type	# Activity
Cell Line	9

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT180	Cell Line	HCT-8	Homo sapiens	IC50	>	10000.0	nM	PMID[491961]
NPT181	Cell Line	Bel-7402	Homo sapiens	IC50	>	10000.0	nM	PMID[491961]
NPT547	Cell Line	BGC-823	Homo sapiens	IC50	>	10000.0	nM	PMID[491961]
NPT81	Cell Line	A549	Homo sapiens	IC50	>	10000.0	nM	PMID[491961]
NPT179	Cell Line	A2780	Homo sapiens	IC50	>	10000.0	nM	PMID[491961]
NPT65	Cell Line	HepG2	Homo sapiens	IC50	>	100000.0	nM	PMID[491962]
NPT397	Cell Line	NCI-H460	Homo sapiens	IC50	>	100000.0	nM	PMID[491962]
NPT83	Cell Line	MCF7	Homo sapiens	IC50	>	100000.0	nM	PMID[491962]
NPT395	Cell Line	SF-268	Homo sapiens	IC50	>	100000.0	nM	PMID[491962]

☑ 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 NPC54988 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	364
0.1-0.2	3456
0.2-0.3	17875
0.3-0.4	13635
0.4-0.5	3143
0.5-0.6	2117
0.6-0.7	1351
0.7-0.8	567
0.8-0.85	127
0.85-0.9	39
0.9-0.95	18
0.95-1	5

Similarity Score	Similarity Level	Natural Product ID
0.9735	High Similarity	NPC279918
0.9671	High Similarity	NPC282231
0.9484	High Similarity	NPC49954
0.9484	High Similarity	NPC474561
0.9423	High Similarity	NPC63751
0.9231	High Similarity	NPC194640
0.9221	High Similarity	NPC469762
0.9202	High Similarity	NPC163055
0.9161	High Similarity	NPC230869
0.9156	High Similarity	NPC469785
0.9114	High Similarity	NPC160105
0.9074	High Similarity	NPC59269
0.8957	High Similarity	NPC248454
0.8909	High Similarity	NPC233936
0.8903	High Similarity	NPC73952
0.8903	High Similarity	NPC469765
0.8903	High Similarity	NPC469763
0.8903	High Similarity	NPC469760
0.8903	High Similarity	NPC259644
0.8903	High Similarity	NPC469786
0.8903	High Similarity	NPC25008
0.8889	High Similarity	NPC314603
0.8868	High Similarity	NPC311276
0.8846	High Similarity	NPC211572
0.8846	High Similarity	NPC75540
0.8846	High Similarity	NPC212376
0.8846	High Similarity	NPC80597
0.8846	High Similarity	NPC70922
0.8834	High Similarity	NPC110500
0.8834	High Similarity	NPC203468
0.8834	High Similarity	NPC149155
0.8827	High Similarity	NPC470498
0.882	High Similarity	NPC201700
0.879	High Similarity	NPC285469
0.878	High Similarity	NPC267885
0.8758	High Similarity	NPC314372
0.875	High Similarity	NPC190296
0.875	High Similarity	NPC40779
0.875	High Similarity	NPC102423
0.8704	High Similarity	NPC78020
0.8675	High Similarity	NPC283219
0.8675	High Similarity	NPC126709
0.8675	High Similarity	NPC248041
0.8647	High Similarity	NPC317030
0.8636	High Similarity	NPC159856
0.8625	High Similarity	NPC131718
0.8614	High Similarity	NPC68354
0.8588	High Similarity	NPC474707
0.858	High Similarity	NPC470508
0.8571	High Similarity	NPC16667
0.8538	High Similarity	NPC204565
0.8529	High Similarity	NPC15102
0.8503	High Similarity	NPC151939
0.8494	Intermediate Similarity	NPC37423
0.8494	Intermediate Similarity	NPC275305
0.8491	Intermediate Similarity	NPC207726
0.8491	Intermediate Similarity	NPC470507
0.8488	Intermediate Similarity	NPC173028
0.8488	Intermediate Similarity	NPC65215
0.8477	Intermediate Similarity	NPC96102
0.8471	Intermediate Similarity	NPC165495
0.8462	Intermediate Similarity	NPC71037
0.8448	Intermediate Similarity	NPC477167
0.8448	Intermediate Similarity	NPC473342
0.8439	Intermediate Similarity	NPC95783
0.8434	Intermediate Similarity	NPC313791
0.8427	Intermediate Similarity	NPC470497
0.8421	Intermediate Similarity	NPC84911
0.8421	Intermediate Similarity	NPC163421
0.8421	Intermediate Similarity	NPC105127
0.8421	Intermediate Similarity	NPC188387
0.8418	Intermediate Similarity	NPC105818
0.8418	Intermediate Similarity	NPC24678
0.8412	Intermediate Similarity	NPC48938
0.8408	Intermediate Similarity	NPC471957
0.8402	Intermediate Similarity	NPC300688
0.8393	Intermediate Similarity	NPC14113
0.8393	Intermediate Similarity	NPC145885
0.8393	Intermediate Similarity	NPC84827
0.8382	Intermediate Similarity	NPC321708
0.8372	Intermediate Similarity	NPC235684
0.8372	Intermediate Similarity	NPC315555
0.8355	Intermediate Similarity	NPC261195
0.8355	Intermediate Similarity	NPC29886
0.8344	Intermediate Similarity	NPC143872
0.8343	Intermediate Similarity	NPC176199
0.8343	Intermediate Similarity	NPC55772
0.8343	Intermediate Similarity	NPC215795
0.8333	Intermediate Similarity	NPC67056
0.8324	Intermediate Similarity	NPC17059
0.8323	Intermediate Similarity	NPC34508
0.8323	Intermediate Similarity	NPC141353
0.8313	Intermediate Similarity	NPC194411
0.8313	Intermediate Similarity	NPC280548
0.8312	Intermediate Similarity	NPC110126
0.8312	Intermediate Similarity	NPC73767
0.8304	Intermediate Similarity	NPC469358
0.8295	Intermediate Similarity	NPC474177
0.8284	Intermediate Similarity	NPC111275
0.8276	Intermediate Similarity	NPC213629
0.8258	Intermediate Similarity	NPC469767
0.8258	Intermediate Similarity	NPC469761
0.8258	Intermediate Similarity	NPC469784
0.8258	Intermediate Similarity	NPC469768
0.8258	Intermediate Similarity	NPC469783
0.8258	Intermediate Similarity	NPC469779
0.8258	Intermediate Similarity	NPC279081
0.8258	Intermediate Similarity	NPC469780
0.8256	Intermediate Similarity	NPC228835
0.8253	Intermediate Similarity	NPC317430
0.825	Intermediate Similarity	NPC216713
0.8249	Intermediate Similarity	NPC133366
0.8239	Intermediate Similarity	NPC37548
0.8235	Intermediate Similarity	NPC213468
0.8235	Intermediate Similarity	NPC11126
0.8232	Intermediate Similarity	NPC476874
0.8221	Intermediate Similarity	NPC135141
0.8221	Intermediate Similarity	NPC92796
0.8214	Intermediate Similarity	NPC472123
0.8212	Intermediate Similarity	NPC473640
0.8212	Intermediate Similarity	NPC470499
0.8212	Intermediate Similarity	NPC82295
0.8208	Intermediate Similarity	NPC314002
0.8205	Intermediate Similarity	NPC469766
0.8198	Intermediate Similarity	NPC220765
0.8167	Intermediate Similarity	NPC100321
0.8166	Intermediate Similarity	NPC472586
0.8161	Intermediate Similarity	NPC94752
0.8156	Intermediate Similarity	NPC229332
0.815	Intermediate Similarity	NPC204717
0.8141	Intermediate Similarity	NPC230002
0.8136	Intermediate Similarity	NPC304187
0.8136	Intermediate Similarity	NPC477166
0.8132	Intermediate Similarity	NPC193761
0.8129	Intermediate Similarity	NPC472443
0.8129	Intermediate Similarity	NPC270009
0.8125	Intermediate Similarity	NPC154339
0.8114	Intermediate Similarity	NPC46580
0.8113	Intermediate Similarity	NPC288838
0.8092	Intermediate Similarity	NPC472108
0.8092	Intermediate Similarity	NPC139291
0.8077	Intermediate Similarity	NPC475506
0.807	Intermediate Similarity	NPC217372
0.807	Intermediate Similarity	NPC183662
0.807	Intermediate Similarity	NPC15573
0.8063	Intermediate Similarity	NPC469811
0.8059	Intermediate Similarity	NPC329688
0.8059	Intermediate Similarity	NPC189812
0.8057	Intermediate Similarity	NPC171171
0.8057	Intermediate Similarity	NPC62749
0.8054	Intermediate Similarity	NPC323927
0.8049	Intermediate Similarity	NPC129721
0.8037	Intermediate Similarity	NPC38736
0.8035	Intermediate Similarity	NPC192270
0.8034	Intermediate Similarity	NPC99666
0.8033	Intermediate Similarity	NPC155143
0.8026	Intermediate Similarity	NPC22079
0.8023	Intermediate Similarity	NPC219336
0.8012	Intermediate Similarity	NPC321911
0.8012	Intermediate Similarity	NPC187951
0.8	Intermediate Similarity	NPC251090
0.8	Intermediate Similarity	NPC63545
0.8	Intermediate Similarity	NPC318065
0.8	Intermediate Similarity	NPC179701
0.8	Intermediate Similarity	NPC206819
0.7989	Intermediate Similarity	NPC472109
0.7989	Intermediate Similarity	NPC472110
0.7989	Intermediate Similarity	NPC472444
0.7989	Intermediate Similarity	NPC267343
0.7987	Intermediate Similarity	NPC242556
0.7976	Intermediate Similarity	NPC49217
0.7975	Intermediate Similarity	NPC200214
0.7965	Intermediate Similarity	NPC293472
0.7965	Intermediate Similarity	NPC184964
0.7963	Intermediate Similarity	NPC53947
0.7957	Intermediate Similarity	NPC54420
0.7956	Intermediate Similarity	NPC262898
0.795	Intermediate Similarity	NPC179787
0.795	Intermediate Similarity	NPC201380
0.7944	Intermediate Similarity	NPC294693
0.7943	Intermediate Similarity	NPC284678
0.7923	Intermediate Similarity	NPC106771
0.7923	Intermediate Similarity	NPC23420
0.7923	Intermediate Similarity	NPC303820
0.7923	Intermediate Similarity	NPC205254
0.7914	Intermediate Similarity	NPC314957
0.7912	Intermediate Similarity	NPC171317
0.7901	Intermediate Similarity	NPC242209
0.7898	Intermediate Similarity	NPC280290
0.7898	Intermediate Similarity	NPC62510
0.7889	Intermediate Similarity	NPC307963
0.7886	Intermediate Similarity	NPC19679
0.7885	Intermediate Similarity	NPC325252
0.788	Intermediate Similarity	NPC475935
0.788	Intermediate Similarity	NPC52909
0.788	Intermediate Similarity	NPC94211
0.7872	Intermediate Similarity	NPC162860
0.7872	Intermediate Similarity	NPC478158
0.7869	Intermediate Similarity	NPC293917
0.7866	Intermediate Similarity	NPC325903

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 NPC54988 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	183
0.1-0.2	580
0.2-0.3	1003
0.3-0.4	1505
0.4-0.5	2714
0.5-0.6	2088
0.6-0.7	871
0.7-0.8	174
0.8-0.85	26
0.85-0.9	6
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.9	High Similarity	NPD4184	Clinical (unspecified phase)
0.8963	High Similarity	NPD6595	Phase 3
0.8834	High Similarity	NPD482	Approved
0.8675	High Similarity	NPD4076	Approved
0.8675	High Similarity	NPD4079	Approved
0.8667	High Similarity	NPD749	Clinical (unspecified phase)
0.8614	High Similarity	NPD3506	Approved
0.8614	High Similarity	NPD3505	Approved
0.8521	High Similarity	NPD2095	Phase 2
0.8521	High Similarity	NPD2094	Phase 2
0.8521	High Similarity	NPD2092	Phase 2
0.8503	High Similarity	NPD2144	Approved
0.8477	Intermediate Similarity	NPD198	Clinical (unspecified phase)
0.8476	Intermediate Similarity	NPD5069	Clinical (unspecified phase)
0.8471	Intermediate Similarity	NPD2096	Phase 2
0.8471	Intermediate Similarity	NPD2091	Phase 2
0.8434	Intermediate Similarity	NPD750	Phase 2
0.8431	Intermediate Similarity	NPD786	Approved
0.843	Intermediate Similarity	NPD8431	Approved
0.8421	Intermediate Similarity	NPD6610	Clinical (unspecified phase)
0.8412	Intermediate Similarity	NPD5728	Clinical (unspecified phase)
0.8393	Intermediate Similarity	NPD6203	Clinical (unspecified phase)
0.8383	Intermediate Similarity	NPD5065	Approved
0.8382	Intermediate Similarity	NPD8110	Clinical (unspecified phase)
0.8353	Intermediate Similarity	NPD3038	Discontinued
0.8323	Intermediate Similarity	NPD1722	Approved
0.8239	Intermediate Similarity	NPD4374	Clinical (unspecified phase)
0.8239	Intermediate Similarity	NPD3100	Discontinued
0.8144	Intermediate Similarity	NPD4638	Approved
0.8144	Intermediate Similarity	NPD4640	Approved
0.8144	Intermediate Similarity	NPD4639	Approved
0.8095	Intermediate Similarity	NPD1325	Approved
0.8095	Intermediate Similarity	NPD1326	Approved
0.809	Intermediate Similarity	NPD5575	Clinical (unspecified phase)
0.8056	Intermediate Similarity	NPD7948	Phase 1
0.7989	Intermediate Similarity	NPD8072	Approved
0.7953	Intermediate Similarity	NPD4128	Approved
0.7946	Intermediate Similarity	NPD8272	Phase 2
0.7903	Intermediate Similarity	NPD7957	Phase 1
0.7903	Intermediate Similarity	NPD7958	Clinical (unspecified phase)
0.7889	Intermediate Similarity	NPD1304	Clinical (unspecified phase)
0.7889	Intermediate Similarity	NPD1038	Approved
0.7874	Intermediate Similarity	NPD8464	Clinical (unspecified phase)
0.7869	Intermediate Similarity	NPD7621	Clinical (unspecified phase)
0.7853	Intermediate Similarity	NPD4463	Approved
0.7853	Intermediate Similarity	NPD2172	Phase 1
0.7853	Intermediate Similarity	NPD4462	Approved
0.7838	Intermediate Similarity	NPD8073	Approved
0.7826	Intermediate Similarity	NPD484	Approved
0.7819	Intermediate Similarity	NPD7947	Clinical (unspecified phase)
0.7816	Intermediate Similarity	NPD8386	Phase 2
0.7809	Intermediate Similarity	NPD3961	Discontinued
0.7807	Intermediate Similarity	NPD4862	Clinical (unspecified phase)
0.7803	Intermediate Similarity	NPD4075	Phase 2
0.7803	Intermediate Similarity	NPD6375	Clinical (unspecified phase)
0.7758	Intermediate Similarity	NPD2837	Discontinued
0.7754	Intermediate Similarity	NPD5901	Discontinued
0.7747	Intermediate Similarity	NPD7944	Discontinued
0.7738	Intermediate Similarity	NPD1403	Approved
0.7738	Intermediate Similarity	NPD1404	Approved
0.7737	Intermediate Similarity	NPD7809	Clinical (unspecified phase)
0.7733	Intermediate Similarity	NPD5934	Clinical (unspecified phase)
0.773	Intermediate Similarity	NPD4703	Approved
0.773	Intermediate Similarity	NPD4702	Approved
0.7719	Intermediate Similarity	NPD5021	Discontinued
0.7696	Intermediate Similarity	NPD7470	Discontinued
0.7672	Intermediate Similarity	NPD8493	Clinical (unspecified phase)
0.7657	Intermediate Similarity	NPD4181	Approved
0.7647	Intermediate Similarity	NPD3323	Discontinued
0.7644	Intermediate Similarity	NPD2928	Phase 2
0.764	Intermediate Similarity	NPD1592	Phase 3
0.7616	Intermediate Similarity	NPD2641	Approved
0.7616	Intermediate Similarity	NPD2185	Clinical (unspecified phase)
0.7616	Intermediate Similarity	NPD2640	Approved
0.7611	Intermediate Similarity	NPD3486	Clinical (unspecified phase)
0.7604	Intermediate Similarity	NPD8013	Clinical (unspecified phase)
0.7597	Intermediate Similarity	NPD992	Clinical (unspecified phase)
0.7597	Intermediate Similarity	NPD991	Phase 2
0.7596	Intermediate Similarity	NPD802	Phase 2
0.7588	Intermediate Similarity	NPD972	Clinical (unspecified phase)
0.7577	Intermediate Similarity	NPD8112	Clinical (unspecified phase)
0.7566	Intermediate Similarity	NPD5426	Phase 3
0.7558	Intermediate Similarity	NPD2639	Approved
0.7558	Intermediate Similarity	NPD2642	Approved
0.7556	Intermediate Similarity	NPD706	Phase 1
0.7552	Intermediate Similarity	NPD7998	Clinical (unspecified phase)
0.7552	Intermediate Similarity	NPD7825	Clinical (unspecified phase)
0.7541	Intermediate Similarity	NPD3404	Approved
0.7538	Intermediate Similarity	NPD5612	Discontinued
0.7529	Intermediate Similarity	NPD3116	Approved
0.7529	Intermediate Similarity	NPD3117	Approved
0.7515	Intermediate Similarity	NPD1661	Suspended
0.75	Intermediate Similarity	NPD2381	Approved
0.75	Intermediate Similarity	NPD2380	Approved
0.75	Intermediate Similarity	NPD2382	Approved
0.75	Intermediate Similarity	NPD5744	Clinical (unspecified phase)
0.7487	Intermediate Similarity	NPD1392	Approved
0.7485	Intermediate Similarity	NPD1853	Clinical (unspecified phase)
0.7485	Intermediate Similarity	NPD8026	Phase 1
0.7474	Intermediate Similarity	NPD8458	Clinical (unspecified phase)
0.7474	Intermediate Similarity	NPD7594	Clinical (unspecified phase)
0.7469	Intermediate Similarity	NPD3943	Clinical (unspecified phase)
0.7459	Intermediate Similarity	NPD7618	Phase 3
0.7459	Intermediate Similarity	NPD6217	Discontinued
0.7459	Intermediate Similarity	NPD7619	Phase 3
0.7447	Intermediate Similarity	NPD4601	Approved
0.7447	Intermediate Similarity	NPD4600	Approved
0.7436	Intermediate Similarity	NPD8488	Clinical (unspecified phase)
0.7432	Intermediate Similarity	NPD4499	Approved
0.7429	Intermediate Similarity	NPD3610	Approved
0.7429	Intermediate Similarity	NPD3609	Approved
0.7414	Intermediate Similarity	NPD5862	Discovery
0.7409	Intermediate Similarity	NPD2125	Clinical (unspecified phase)
0.7401	Intermediate Similarity	NPD5100	Phase 3
0.7396	Intermediate Similarity	NPD8410	Clinical (unspecified phase)
0.7378	Intermediate Similarity	NPD4637	Clinical (unspecified phase)
0.736	Intermediate Similarity	NPD8123	Approved
0.736	Intermediate Similarity	NPD8122	Approved
0.7353	Intermediate Similarity	NPD276	Clinical (unspecified phase)
0.7348	Intermediate Similarity	NPD3607	Clinical (unspecified phase)
0.7341	Intermediate Similarity	NPD5138	Approved
0.7341	Intermediate Similarity	NPD5140	Approved
0.7337	Intermediate Similarity	NPD5117	Phase 2
0.7333	Intermediate Similarity	NPD5066	Phase 2
0.7333	Intermediate Similarity	NPD5254	Discontinued
0.7333	Intermediate Similarity	NPD5067	Phase 2
0.733	Intermediate Similarity	NPD2121	Clinical (unspecified phase)
0.7326	Intermediate Similarity	NPD7818	Clinical (unspecified phase)
0.7323	Intermediate Similarity	NPD8406	Clinical (unspecified phase)
0.7322	Intermediate Similarity	NPD5590	Clinical (unspecified phase)
0.7314	Intermediate Similarity	NPD4779	Clinical (unspecified phase)
0.7308	Intermediate Similarity	NPD5555	Phase 1
0.7306	Intermediate Similarity	NPD6838	Clinical (unspecified phase)
0.7302	Intermediate Similarity	NPD3825	Phase 3
0.7297	Intermediate Similarity	NPD6180	Clinical (unspecified phase)
0.7296	Intermediate Similarity	NPD3330	Phase 1
0.7293	Intermediate Similarity	NPD5105	Approved
0.7293	Intermediate Similarity	NPD5596	Phase 2
0.7293	Intermediate Similarity	NPD5106	Approved
0.7288	Intermediate Similarity	NPD966	Clinical (unspecified phase)
0.7286	Intermediate Similarity	NPD8405	Clinical (unspecified phase)
0.7284	Intermediate Similarity	NPD1262	Discovery
0.7278	Intermediate Similarity	NPD6277	Clinical (unspecified phase)
0.7277	Intermediate Similarity	NPD5721	Clinical (unspecified phase)
0.7273	Intermediate Similarity	NPD3717	Discontinued
0.7267	Intermediate Similarity	NPD5255	Approved
0.7263	Intermediate Similarity	NPD1272	Clinical (unspecified phase)
0.7246	Intermediate Similarity	NPD1683	Approved
0.7243	Intermediate Similarity	NPD6281	Approved
0.7235	Intermediate Similarity	NPD2012	Clinical (unspecified phase)
0.7233	Intermediate Similarity	NPD3475	Approved
0.7233	Intermediate Similarity	NPD3476	Approved
0.7229	Intermediate Similarity	NPD751	Clinical (unspecified phase)
0.7229	Intermediate Similarity	NPD3813	Approved
0.7228	Intermediate Similarity	NPD3002	Clinical (unspecified phase)
0.7228	Intermediate Similarity	NPD6141	Clinical (unspecified phase)
0.7225	Intermediate Similarity	NPD7903	Clinical (unspecified phase)
0.7222	Intermediate Similarity	NPD8037	Clinical (unspecified phase)
0.7222	Intermediate Similarity	NPD8036	Clinical (unspecified phase)
0.7216	Intermediate Similarity	NPD2844	Phase 3
0.7209	Intermediate Similarity	NPD4671	Clinical (unspecified phase)
0.7209	Intermediate Similarity	NPD1192	Clinical (unspecified phase)
0.7209	Intermediate Similarity	NPD4670	Clinical (unspecified phase)
0.7209	Intermediate Similarity	NPD4669	Clinical (unspecified phase)
0.7208	Intermediate Similarity	NPD8093	Discontinued
0.7202	Intermediate Similarity	NPD4547	Phase 3
0.7196	Intermediate Similarity	NPD6664	Approved
0.7191	Intermediate Similarity	NPD4112	Clinical (unspecified phase)
0.7186	Intermediate Similarity	NPD6803	Clinical (unspecified phase)
0.7179	Intermediate Similarity	NPD2509	Approved
0.7179	Intermediate Similarity	NPD2510	Approved
0.7176	Intermediate Similarity	NPD6476	Clinical (unspecified phase)
0.7176	Intermediate Similarity	NPD6158	Phase 2
0.7174	Intermediate Similarity	NPD4426	Clinical (unspecified phase)
0.717	Intermediate Similarity	NPD3654	Approved
0.7169	Intermediate Similarity	NPD2006	Phase 2
0.7169	Intermediate Similarity	NPD2007	Clinical (unspecified phase)
0.7165	Intermediate Similarity	NPD3003	Approved
0.716	Intermediate Similarity	NPD2430	Phase 2
0.716	Intermediate Similarity	NPD1183	Approved
0.7159	Intermediate Similarity	NPD425	Approved
0.7159	Intermediate Similarity	NPD424	Approved
0.7158	Intermediate Similarity	NPD6178	Phase 3
0.7152	Intermediate Similarity	NPD2118	Approved
0.7152	Intermediate Similarity	NPD2119	Approved
0.7151	Intermediate Similarity	NPD2580	Discontinued
0.7151	Intermediate Similarity	NPD473	Clinical (unspecified phase)
0.7143	Intermediate Similarity	NPD6148	Clinical (unspecified phase)
0.7143	Intermediate Similarity	NPD8129	Discovery
0.7136	Intermediate Similarity	NPD7970	Approved
0.7136	Intermediate Similarity	NPD7971	Clinical (unspecified phase)
0.7135	Intermediate Similarity	NPD2383	Phase 1
0.7134	Intermediate Similarity	NPD2896	Discontinued
0.7128	Intermediate Similarity	NPD8322	Phase 2
0.712	Intermediate Similarity	NPD1768	Approved
0.7112	Intermediate Similarity	NPD5913	Phase 3
0.7112	Intermediate Similarity	NPD5912	Clinical (unspecified phase)
0.7112	Intermediate Similarity	NPD4699	Discontinued
0.711	Intermediate Similarity	NPD2582	Approved
0.711	Intermediate Similarity	NPD2581	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