NPASS Compound

Structure

NPC250835 OpenBabel07101719132D 42 49 0 0 1 0 0 0 0 0999 V2000 3.6136 -0.8745 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5684 -1.4769 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4829 0.5961 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3929 -0.3122 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2664 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9085 1.3866 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3300 -0.3690 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.2791 -0.9140 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.8817 -0.0214 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9501 0.0986 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7673 -2.3403 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9434 1.5395 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5395 -0.9434 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7048 -1.7046 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9099 0.0808 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0068 -3.2334 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4559 -1.7528 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3729 0.2766 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1700 -2.4303 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1529 0.9651 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3429 -2.0523 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1606 -3.7220 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -1.5811 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6218 -0.3020 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1500 -1.8414 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5744 -0.7905 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 6.7330 -1.6024 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0068 -2.2563 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6218 -1.2791 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7756 -1.7677 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 6.3355 -0.7098 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1606 -1.7677 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3143 -2.2563 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9293 -0.3020 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.9293 -1.2791 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.7756 0.1866 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 5.3637 -0.8119 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1.5928 -2.2523 0.0000 N 0 0 3 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 N 0 0 3 0 0 0 0 0 0 0 0 0 4.3143 -3.2334 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1.2298 0.9972 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4681 -3.7220 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 1 4 2 0 0 0 0 2 5 1 0 0 0 0 3 6 1 0 0 0 0 3 7 1 0 0 0 0 4 10 1 0 0 0 0 5 11 1 0 0 0 0 6 12 1 0 0 0 0 7 13 2 0 0 0 0 8 9 2 0 0 0 0 8 14 1 0 0 0 0 9 15 1 0 0 0 0 10 18 1 0 0 0 0 11 19 1 0 0 0 0 12 20 1 0 0 0 0 13 26 1 0 0 0 0 14 27 2 0 0 0 0 15 31 2 0 0 0 0 16 22 2 0 0 0 0 16 28 1 0 0 0 0 17 21 1 0 0 0 0 17 30 1 0 0 0 0 18 36 1 0 0 0 0 19 38 1 0 0 0 0 20 39 1 0 0 0 0 21 38 1 0 0 0 0 22 40 1 0 0 0 0 23 26 1 0 0 0 0 24 29 2 0 0 0 0 24 36 1 0 0 0 0 25 35 1 0 0 0 0 25 38 1 0 0 0 0 26 39 1 6 0 0 0 27 28 1 0 0 0 0 27 31 1 0 0 0 0 28 32 2 0 0 0 0 29 30 1 0 0 0 0 29 33 1 0 0 0 0 30 35 1 1 0 0 0 31 37 1 0 0 0 0 32 33 1 0 0 0 0 32 37 1 0 0 0 0 33 40 2 0 0 0 0 34 35 1 1 0 0 0 34 36 1 0 0 0 0 34 39 1 0 0 0 0 35 23 1 1 0 0 0 36 41 1 1 0 0 0 40 42 2 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	564.35
Volume:	600.6
LogP:	3.977
LogD:	3.597
LogS:	-3.213
# Rotatable Bonds:	1
TPSA:	69.44
# H-Bond Aceptor:	6
# H-Bond Donor:	2
# Rings:	8
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.213
Synthetic Accessibility Score:	6.74
Fsp3:	0.528
Lipinski Rule-of-5:	Accepted
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:	-5.354
MDCK Permeability:	2.9787648600176908e-05
Pgp-inhibitor:	0.789
Pgp-substrate:	0.93
Human Intestinal Absorption (HIA):	0.248
20% Bioavailability (F20%):	0.999
30% Bioavailability (F30%):	0.781

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.518
Plasma Protein Binding (PPB):	94.21288299560547%
Volume Distribution (VD):	1.495
Pgp-substrate:	4.193818092346191%

ADMET: Metabolism

CYP1A2-inhibitor:	0.075
CYP1A2-substrate:	0.946
CYP2C19-inhibitor:	0.061
CYP2C19-substrate:	0.068
CYP2C9-inhibitor:	0.034
CYP2C9-substrate:	0.039
CYP2D6-inhibitor:	0.892
CYP2D6-substrate:	0.868
CYP3A4-inhibitor:	0.175
CYP3A4-substrate:	0.612

ADMET: Excretion

Clearance (CL):	6.086
Half-life (T1/2):	0.319

ADMET: Toxicity

hERG Blockers:	0.908
Human Hepatotoxicity (H-HT):	0.936
Drug-inuced Liver Injury (DILI):	0.079
AMES Toxicity:	0.739
Rat Oral Acute Toxicity:	0.704
Maximum Recommended Daily Dose:	0.92
Skin Sensitization:	0.919
Carcinogencity:	0.077
Eye Corrosion:	0.003
Eye Irritation:	0.008
Respiratory Toxicity:	0.886

Download Data

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

Natural Product: NPC250835

Natural Product ID:	NPC250835
*Common Name:**	AQHDHZMKBBWVQD-MKYGIPPKSA-N
IUPAC Name:	n.a.
Synonyms:	Manzamine A N-Oxide
Standard InCHIKey:	AQHDHZMKBBWVQD-MKYGIPPKSA-N
Standard InCHI:	InChI=1S/C36H44N4O2/c41-36-18-10-4-1-2-5-11-19-38-21-17-30(35(25-38)23-26-13-7-3-6-12-20-39(26)34(35)36)29(24-36)33-32-28(16-22-40(33)42)27-14-8-9-15-31(27)37-32/h1,4,7-9,13-16,22,24,26,30,34,37,41H,2-3,5-6,10-12,17-21,23,25H2/b4-1-,13-7-/t26-,30-,34+,35-,36-/m0/s1
SMILES:	C1=CCC[C@@]2(C=C([C@@H]3CCN(CCCC1)C[C@]13C[C@@H]3C=CCCCCN3[C@@H]21)c1c2c(ccn1=O)c1ccccc1[nH]2)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL500612
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000279] Alkaloids and derivatives [CHEMONTID:0001140] Harmala alkaloids

*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
NPO33280	Acanthostrongylophora sp.	Species	Petrosiidae	Eukaryota	n.a.	n.a.	n.a.	PMID[15332848]
NPO33280	Acanthostrongylophora sp.	Species	Petrosiidae	Eukaryota	n.a.	collected from vertical slopes between 33 and 40 m from Knife Cape Manado, Indonesia	n.a.	PMID[16872140]
NPO33280	Acanthostrongylophora sp.	Species	Petrosiidae	Eukaryota	n.a.	collected from vertical slopes between 33 and 40 m from Knife Cape Manado, Indonesia	2004-Mar	PMID[16872140]
NPO33280	Acanthostrongylophora sp.	Species	Petrosiidae	Eukaryota	n.a.	Indonesian	n.a.	PMID[16872140]
NPO33280	Acanthostrongylophora sp.	Species	Petrosiidae	Eukaryota	n.a.	collected from vertical slopes between 33 and 40 m from Knife Cape Manado, Indonesia	2002-May	PMID[16872140]
NPO33280	Acanthostrongylophora sp.	Species	Petrosiidae	Eukaryota	n.a.	n.a.	n.a.	PMID[28452477]
NPO33515	xestospongia ashmorica	Species	Petrosiidae	Eukaryota	n.a.	Philippine	n.a.	PMID[8946747]

☑ 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
ED50	1
IC50	7
MIC	2
Others	3

Activity Type	# Activity
Cell Line	2
Organism	11

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT1864	Cell Line	L5178Y	Mus musculus	ED50	=	1.6	ug ml-1	PMID[524540]
NPT189	Cell Line	Vero	Chlorocebus aethiops	Activity	=	4.2	ug ml-1	PMID[524541]
NPT776	Organism	Spodoptera littoralis	Spodoptera littoralis	Inhibition	=	9.5	%	PMID[524540]
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	IC50	=	0.011	ug.mL-1	PMID[524541]
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	IC50	=	0.013	ug.mL-1	PMID[524541]
NPT633	Organism	Leishmania donovani	Leishmania donovani	IC50	=	1.1	ug.mL-1	PMID[524541]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	IC50	=	0.5	ug.mL-1	PMID[524541]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	IC50	=	0.4	ug.mL-1	PMID[524541]
NPT85	Organism	Filobasidiella neoformans	Cryptococcus neoformans	IC50	=	1.0	ug.mL-1	PMID[524541]
NPT86	Organism	Mycobacterium intracellulare	Mycobacterium intracellulare	IC50	=	0.2	ug.mL-1	PMID[524541]
NPT633	Organism	Leishmania donovani	Leishmania donovani	IC90	=	3.8	ug.mL-1	PMID[524541]
NPT88	Organism	Mycobacterium tuberculosis	Mycobacterium tuberculosis	MIC	=	3.9	ug.mL-1	PMID[524541]
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	MIC	=	11.0	ug.mL-1	PMID[524542]

☑ 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 NPC250835 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	544
0.1-0.2	2674
0.2-0.3	20663
0.3-0.4	11644
0.4-0.5	3098
0.5-0.6	2093
0.6-0.7	1507
0.7-0.8	439
0.8-0.85	13
0.85-0.9	12
0.9-0.95	6
0.95-1	4

Similarity Score	Similarity Level	Natural Product ID
0.9632	High Similarity	NPC166492
0.9632	High Similarity	NPC473362
0.9476	High Similarity	NPC475288
0.911	High Similarity	NPC265576
0.9055	High Similarity	NPC473310
0.8958	High Similarity	NPC232130
0.895	High Similarity	NPC473757
0.8889	High Similarity	NPC6215
0.8861	High Similarity	NPC472027
0.8829	High Similarity	NPC471506
0.8673	High Similarity	NPC476451
0.8619	High Similarity	NPC476492
0.8531	High Similarity	NPC476491
0.8396	Intermediate Similarity	NPC909
0.8396	Intermediate Similarity	NPC475338
0.8357	Intermediate Similarity	NPC475258
0.8349	Intermediate Similarity	NPC41679
0.8251	Intermediate Similarity	NPC471891
0.819	Intermediate Similarity	NPC81175
0.8153	Intermediate Similarity	NPC473312
0.8057	Intermediate Similarity	NPC251936
0.8053	Intermediate Similarity	NPC471564
0.797	Intermediate Similarity	NPC15102
0.7948	Intermediate Similarity	NPC476493
0.7905	Intermediate Similarity	NPC475422
0.785	Intermediate Similarity	NPC476041
0.785	Intermediate Similarity	NPC304926
0.781	Intermediate Similarity	NPC87755
0.7755	Intermediate Similarity	NPC59269
0.7667	Intermediate Similarity	NPC475070
0.7665	Intermediate Similarity	NPC477861
0.7659	Intermediate Similarity	NPC133366
0.765	Intermediate Similarity	NPC472294
0.7614	Intermediate Similarity	NPC280852
0.76	Intermediate Similarity	NPC48938
0.7586	Intermediate Similarity	NPC213629
0.7577	Intermediate Similarity	NPC160105
0.7569	Intermediate Similarity	NPC477714
0.7559	Intermediate Similarity	NPC314957
0.7546	Intermediate Similarity	NPC475602
0.7539	Intermediate Similarity	NPC236711
0.7538	Intermediate Similarity	NPC63751
0.7538	Intermediate Similarity	NPC317430
0.7524	Intermediate Similarity	NPC474177
0.7523	Intermediate Similarity	NPC477715
0.7513	Intermediate Similarity	NPC314603
0.7488	Intermediate Similarity	NPC62749
0.7488	Intermediate Similarity	NPC5145
0.7488	Intermediate Similarity	NPC126066
0.7487	Intermediate Similarity	NPC474561
0.7487	Intermediate Similarity	NPC49954
0.7476	Intermediate Similarity	NPC106771
0.7476	Intermediate Similarity	NPC303820
0.7476	Intermediate Similarity	NPC205254
0.7476	Intermediate Similarity	NPC23420
0.7463	Intermediate Similarity	NPC95783
0.7441	Intermediate Similarity	NPC94211
0.7441	Intermediate Similarity	NPC52909
0.7441	Intermediate Similarity	NPC475935
0.7429	Intermediate Similarity	NPC100321
0.7424	Intermediate Similarity	NPC472123
0.7422	Intermediate Similarity	NPC314954
0.7415	Intermediate Similarity	NPC173028
0.7415	Intermediate Similarity	NPC65215
0.7409	Intermediate Similarity	NPC92796
0.7409	Intermediate Similarity	NPC135141
0.7402	Intermediate Similarity	NPC94752
0.7391	Intermediate Similarity	NPC324149
0.7381	Intermediate Similarity	NPC473640
0.7381	Intermediate Similarity	NPC171317
0.7371	Intermediate Similarity	NPC279918
0.7366	Intermediate Similarity	NPC204565
0.7366	Intermediate Similarity	NPC317030
0.7361	Intermediate Similarity	NPC476116
0.736	Intermediate Similarity	NPC201700
0.7358	Intermediate Similarity	NPC475506
0.7346	Intermediate Similarity	NPC293917
0.7344	Intermediate Similarity	NPC211572
0.7344	Intermediate Similarity	NPC80597
0.7344	Intermediate Similarity	NPC70922
0.7344	Intermediate Similarity	NPC75540
0.7344	Intermediate Similarity	NPC212376
0.734	Intermediate Similarity	NPC139291
0.734	Intermediate Similarity	NPC472108
0.7333	Intermediate Similarity	NPC282231
0.733	Intermediate Similarity	NPC321708
0.7324	Intermediate Similarity	NPC155143
0.7321	Intermediate Similarity	NPC157828
0.7321	Intermediate Similarity	NPC195239
0.7317	Intermediate Similarity	NPC474707
0.7313	Intermediate Similarity	NPC151939
0.73	Intermediate Similarity	NPC189812
0.73	Intermediate Similarity	NPC329688
0.7299	Intermediate Similarity	NPC192315
0.7296	Intermediate Similarity	NPC194640
0.7296	Intermediate Similarity	NPC317105
0.7292	Intermediate Similarity	NPC469786
0.7292	Intermediate Similarity	NPC73952
0.7292	Intermediate Similarity	NPC469765
0.7292	Intermediate Similarity	NPC25008
0.7292	Intermediate Similarity	NPC469763
0.7292	Intermediate Similarity	NPC469760
0.7292	Intermediate Similarity	NPC259644
0.7291	Intermediate Similarity	NPC233936
0.7291	Intermediate Similarity	NPC314394
0.729	Intermediate Similarity	NPC98715
0.7286	Intermediate Similarity	NPC11445
0.7282	Intermediate Similarity	NPC17059
0.7281	Intermediate Similarity	NPC162860
0.7281	Intermediate Similarity	NPC271862
0.7277	Intermediate Similarity	NPC133261
0.7277	Intermediate Similarity	NPC300183
0.7269	Intermediate Similarity	NPC54420
0.7269	Intermediate Similarity	NPC253580
0.7268	Intermediate Similarity	NPC469762
0.7264	Intermediate Similarity	NPC476167
0.7264	Intermediate Similarity	NPC203754
0.7264	Intermediate Similarity	NPC150048
0.726	Intermediate Similarity	NPC473763
0.726	Intermediate Similarity	NPC117244
0.7256	Intermediate Similarity	NPC470500
0.7255	Intermediate Similarity	NPC19679
0.7251	Intermediate Similarity	NPC229332
0.7245	Intermediate Similarity	NPC16667
0.7243	Intermediate Similarity	NPC193761
0.7241	Intermediate Similarity	NPC300688
0.724	Intermediate Similarity	NPC183407
0.7238	Intermediate Similarity	NPC195314
0.7236	Intermediate Similarity	NPC280548
0.7232	Intermediate Similarity	NPC474896
0.723	Intermediate Similarity	NPC252338
0.7229	Intermediate Similarity	NPC295228
0.7228	Intermediate Similarity	NPC326575
0.7225	Intermediate Similarity	NPC470126
0.7222	Intermediate Similarity	NPC54988
0.722	Intermediate Similarity	NPC165495
0.722	Intermediate Similarity	NPC193267
0.722	Intermediate Similarity	NPC213530
0.722	Intermediate Similarity	NPC284678
0.7216	Intermediate Similarity	NPC469785
0.7216	Intermediate Similarity	NPC285469
0.7211	Intermediate Similarity	NPC63545
0.7208	Intermediate Similarity	NPC311276
0.7202	Intermediate Similarity	NPC478158
0.7202	Intermediate Similarity	NPC325903
0.72	Intermediate Similarity	NPC155444
0.72	Intermediate Similarity	NPC31097
0.7194	Intermediate Similarity	NPC229173
0.7194	Intermediate Similarity	NPC131718
0.7193	Intermediate Similarity	NPC33949
0.7192	Intermediate Similarity	NPC176199
0.7192	Intermediate Similarity	NPC215795
0.7189	Intermediate Similarity	NPC46225
0.7189	Intermediate Similarity	NPC225821
0.7188	Intermediate Similarity	NPC24678
0.7188	Intermediate Similarity	NPC105818
0.7182	Intermediate Similarity	NPC75634
0.7182	Intermediate Similarity	NPC110602
0.7182	Intermediate Similarity	NPC75726
0.7182	Intermediate Similarity	NPC87856
0.7182	Intermediate Similarity	NPC151976
0.7182	Intermediate Similarity	NPC31385
0.7179	Intermediate Similarity	NPC129721
0.7176	Intermediate Similarity	NPC470505
0.7173	Intermediate Similarity	NPC201380
0.7173	Intermediate Similarity	NPC469811
0.7173	Intermediate Similarity	NPC179787
0.7171	Intermediate Similarity	NPC472109
0.7171	Intermediate Similarity	NPC472110
0.7168	Intermediate Similarity	NPC229893
0.7163	Intermediate Similarity	NPC473761
0.7162	Intermediate Similarity	NPC477175
0.7162	Intermediate Similarity	NPC326363
0.7162	Intermediate Similarity	NPC470730
0.7156	Intermediate Similarity	NPC127677
0.7156	Intermediate Similarity	NPC258062
0.715	Intermediate Similarity	NPC249040
0.715	Intermediate Similarity	NPC194411
0.7149	Intermediate Similarity	NPC221100
0.7149	Intermediate Similarity	NPC267965
0.7149	Intermediate Similarity	NPC234078
0.7143	Intermediate Similarity	NPC68354
0.7143	Intermediate Similarity	NPC474880
0.7143	Intermediate Similarity	NPC67056
0.7143	Intermediate Similarity	NPC475990
0.7143	Intermediate Similarity	NPC230869
0.7143	Intermediate Similarity	NPC221786
0.7137	Intermediate Similarity	NPC313884
0.7137	Intermediate Similarity	NPC98371
0.7136	Intermediate Similarity	NPC320968
0.7136	Intermediate Similarity	NPC470499
0.7136	Intermediate Similarity	NPC131887
0.7135	Intermediate Similarity	NPC321911
0.713	Intermediate Similarity	NPC475859
0.713	Intermediate Similarity	NPC475969
0.7129	Intermediate Similarity	NPC231536
0.7124	Intermediate Similarity	NPC162748
0.7123	Intermediate Similarity	NPC223791
0.7123	Intermediate Similarity	NPC107077
0.7121	Intermediate Similarity	NPC40779

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 NPC250835 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	247
0.1-0.2	562
0.2-0.3	998
0.3-0.4	1893
0.4-0.5	2566
0.5-0.6	1911
0.6-0.7	879
0.7-0.8	94
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
0.797	Intermediate Similarity	NPD6610	Clinical (unspecified phase)
0.7755	Intermediate Similarity	NPD6203	Clinical (unspecified phase)
0.7653	Intermediate Similarity	NPD5065	Approved
0.7619	Intermediate Similarity	NPD4886	Phase 2
0.759	Intermediate Similarity	NPD4184	Clinical (unspecified phase)
0.7588	Intermediate Similarity	NPD6595	Phase 3
0.7545	Intermediate Similarity	NPD7824	Approved
0.7537	Intermediate Similarity	NPD8431	Approved
0.7465	Intermediate Similarity	NPD8488	Clinical (unspecified phase)
0.7455	Intermediate Similarity	NPD7731	Approved
0.7455	Intermediate Similarity	NPD7730	Approved
0.7444	Intermediate Similarity	NPD7271	Approved
0.7419	Intermediate Similarity	NPD8458	Clinical (unspecified phase)
0.7395	Intermediate Similarity	NPD7666	Phase 3
0.7395	Intermediate Similarity	NPD7665	Phase 2
0.7368	Intermediate Similarity	NPD7791	Approved
0.7368	Intermediate Similarity	NPD7952	Approved
0.7368	Intermediate Similarity	NPD7790	Approved
0.7368	Intermediate Similarity	NPD7953	Approved
0.7368	Intermediate Similarity	NPD7950	Approved
0.7368	Intermediate Similarity	NPD7951	Approved
0.7368	Intermediate Similarity	NPD7789	Approved
0.736	Intermediate Similarity	NPD5069	Clinical (unspecified phase)
0.735	Intermediate Similarity	NPD6375	Clinical (unspecified phase)
0.7349	Intermediate Similarity	NPD6838	Clinical (unspecified phase)
0.7349	Intermediate Similarity	NPD8493	Clinical (unspecified phase)
0.7347	Intermediate Similarity	NPD5744	Clinical (unspecified phase)
0.7346	Intermediate Similarity	NPD7621	Clinical (unspecified phase)
0.7339	Intermediate Similarity	NPD7594	Clinical (unspecified phase)
0.7333	Intermediate Similarity	NPD7948	Phase 1
0.733	Intermediate Similarity	NPD8110	Clinical (unspecified phase)
0.7327	Intermediate Similarity	NPD6277	Clinical (unspecified phase)
0.7327	Intermediate Similarity	NPD8464	Clinical (unspecified phase)
0.7315	Intermediate Similarity	NPD7947	Clinical (unspecified phase)
0.7282	Intermediate Similarity	NPD3961	Discontinued
0.7282	Intermediate Similarity	NPD3486	Clinical (unspecified phase)
0.726	Intermediate Similarity	NPD3330	Phase 1
0.7256	Intermediate Similarity	NPD5426	Phase 3
0.7255	Intermediate Similarity	NPD5728	Clinical (unspecified phase)
0.7228	Intermediate Similarity	NPD4181	Approved
0.7225	Intermediate Similarity	NPD3404	Approved
0.7207	Intermediate Similarity	NPD7823	Clinical (unspecified phase)
0.7202	Intermediate Similarity	NPD2837	Discontinued
0.7192	Intermediate Similarity	NPD4076	Approved
0.7192	Intermediate Similarity	NPD4079	Approved
0.7189	Intermediate Similarity	NPD8410	Clinical (unspecified phase)
0.7182	Intermediate Similarity	NPD8093	Discontinued
0.7181	Intermediate Similarity	NPD6352	Phase 2
0.7156	Intermediate Similarity	NPD7618	Phase 3
0.7156	Intermediate Similarity	NPD7619	Phase 3
0.7143	Intermediate Similarity	NPD3506	Approved
0.7143	Intermediate Similarity	NPD2144	Approved
0.7143	Intermediate Similarity	NPD5255	Approved
0.7143	Intermediate Similarity	NPD7958	Clinical (unspecified phase)
0.7143	Intermediate Similarity	NPD7957	Phase 1
0.7143	Intermediate Similarity	NPD3505	Approved
0.7137	Intermediate Similarity	NPD6976	Clinical (unspecified phase)
0.7122	Intermediate Similarity	NPD3038	Discontinued
0.7121	Intermediate Similarity	NPD3323	Discontinued
0.7118	Intermediate Similarity	NPD7781	Approved
0.7118	Intermediate Similarity	NPD7780	Approved
0.7109	Intermediate Similarity	NPD5575	Clinical (unspecified phase)
0.7108	Intermediate Similarity	NPD8386	Phase 2
0.7103	Intermediate Similarity	NPD7000	Clinical (unspecified phase)
0.7103	Intermediate Similarity	NPD6999	Discontinued
0.7098	Intermediate Similarity	NPD8405	Clinical (unspecified phase)
0.7074	Intermediate Similarity	NPD6165	Phase 2
0.7074	Intermediate Similarity	NPD6977	Clinical (unspecified phase)
0.7074	Intermediate Similarity	NPD6164	Phase 2
0.7074	Intermediate Similarity	NPD6978	Phase 2
0.7062	Intermediate Similarity	NPD4615	Phase 2
0.7059	Intermediate Similarity	NPD7470	Discontinued
0.7053	Intermediate Similarity	NPD6178	Phase 3
0.7044	Intermediate Similarity	NPD4128	Approved
0.7042	Intermediate Similarity	NPD6449	Clinical (unspecified phase)
0.7037	Intermediate Similarity	NPD5017	Discontinued
0.7031	Intermediate Similarity	NPD7469	Discontinued
0.703	Intermediate Similarity	NPD5934	Clinical (unspecified phase)
0.7019	Intermediate Similarity	NPD6227	Discontinued
0.7018	Intermediate Similarity	NPD7712	Clinical (unspecified phase)
0.7015	Intermediate Similarity	NPD4779	Clinical (unspecified phase)
0.7014	Intermediate Similarity	NPD7809	Clinical (unspecified phase)
0.701	Intermediate Similarity	NPD2172	Phase 1
0.7009	Intermediate Similarity	NPD3830	Phase 1
0.7005	Intermediate Similarity	NPD2094	Phase 2
0.7005	Intermediate Similarity	NPD2095	Phase 2
0.7005	Intermediate Similarity	NPD2092	Phase 2
0.6996	Remote Similarity	NPD8094	Discontinued
0.6991	Remote Similarity	NPD4600	Approved
0.6991	Remote Similarity	NPD4601	Approved
0.6986	Remote Similarity	NPD706	Phase 1
0.6982	Remote Similarity	NPD8013	Clinical (unspecified phase)
0.698	Remote Similarity	NPD1325	Approved
0.698	Remote Similarity	NPD1326	Approved
0.6978	Remote Similarity	NPD8406	Clinical (unspecified phase)
0.6971	Remote Similarity	NPD2096	Phase 2
0.6971	Remote Similarity	NPD2091	Phase 2
0.6968	Remote Similarity	NPD6545	Clinical (unspecified phase)
0.6967	Remote Similarity	NPD6281	Approved
0.6963	Remote Similarity	NPD7818	Clinical (unspecified phase)
0.6961	Remote Similarity	NPD482	Approved
0.6957	Remote Similarity	NPD7867	Phase 1
0.6952	Remote Similarity	NPD8020	Approved
0.6952	Remote Similarity	NPD8021	Approved
0.6952	Remote Similarity	NPD6141	Clinical (unspecified phase)
0.6951	Remote Similarity	NPD4852	Phase 2
0.6941	Remote Similarity	NPD5901	Discontinued
0.6941	Remote Similarity	NPD8272	Phase 2
0.6938	Remote Similarity	NPD3082	Discontinued
0.6937	Remote Similarity	NPD3014	Clinical (unspecified phase)
0.6937	Remote Similarity	NPD3013	Phase 3
0.6934	Remote Similarity	NPD6630	Clinical (unspecified phase)
0.6933	Remote Similarity	NPD7112	Discontinued
0.693	Remote Similarity	NPD6615	Clinical (unspecified phase)
0.6927	Remote Similarity	NPD8073	Approved
0.6923	Remote Similarity	NPD7415	Suspended
0.6923	Remote Similarity	NPD4463	Approved
0.6923	Remote Similarity	NPD4462	Approved
0.6916	Remote Similarity	NPD4999	Phase 3
0.6916	Remote Similarity	NPD4998	Phase 3
0.6912	Remote Similarity	NPD4112	Clinical (unspecified phase)
0.6911	Remote Similarity	NPD1722	Approved
0.6907	Remote Similarity	NPD4703	Approved
0.6907	Remote Similarity	NPD4547	Phase 3
0.6907	Remote Similarity	NPD4702	Approved
0.6903	Remote Similarity	NPD7423	Phase 2
0.6893	Remote Similarity	NPD8123	Approved
0.6893	Remote Similarity	NPD8122	Approved
0.6892	Remote Similarity	NPD2125	Clinical (unspecified phase)
0.6878	Remote Similarity	NPD8322	Phase 2
0.6875	Remote Similarity	NPD8408	Discontinued
0.687	Remote Similarity	NPD6849	Phase 2
0.687	Remote Similarity	NPD6850	Phase 2
0.6866	Remote Similarity	NPD5140	Approved
0.6866	Remote Similarity	NPD5138	Approved
0.6861	Remote Similarity	NPD7998	Clinical (unspecified phase)
0.6852	Remote Similarity	NPD6664	Approved
0.6847	Remote Similarity	NPD5862	Discovery
0.6847	Remote Similarity	NPD4640	Approved
0.6847	Remote Similarity	NPD4639	Approved
0.6847	Remote Similarity	NPD4638	Approved
0.6847	Remote Similarity	NPD2390	Clinical (unspecified phase)
0.6847	Remote Similarity	NPD4612	Discontinued
0.6845	Remote Similarity	NPD5100	Phase 3
0.6845	Remote Similarity	NPD2380	Approved
0.6845	Remote Similarity	NPD4075	Phase 2
0.6845	Remote Similarity	NPD2381	Approved
0.6845	Remote Similarity	NPD2382	Approved
0.6845	Remote Similarity	NPD749	Clinical (unspecified phase)
0.6842	Remote Similarity	NPD5596	Phase 2
0.684	Remote Similarity	NPD6363	Clinical (unspecified phase)
0.684	Remote Similarity	NPD6965	Clinical (unspecified phase)
0.6837	Remote Similarity	NPD7944	Discontinued
0.6833	Remote Similarity	NPD7001	Phase 3
0.6832	Remote Similarity	NPD2720	Phase 1
0.6832	Remote Similarity	NPD2719	Clinical (unspecified phase)
0.682	Remote Similarity	NPD7204	Clinical (unspecified phase)
0.6818	Remote Similarity	NPD8072	Approved
0.6816	Remote Similarity	NPD1853	Clinical (unspecified phase)
0.6814	Remote Similarity	NPD7073	Clinical (unspecified phase)
0.6814	Remote Similarity	NPD8112	Clinical (unspecified phase)
0.681	Remote Similarity	NPD7711	Discontinued
0.681	Remote Similarity	NPD4957	Phase 2
0.681	Remote Similarity	NPD7603	Discontinued
0.6808	Remote Similarity	NPD8063	Discontinued
0.6804	Remote Similarity	NPD7903	Clinical (unspecified phase)
0.6797	Remote Similarity	NPD7202	Clinical (unspecified phase)
0.6792	Remote Similarity	NPD7394	Phase 2
0.6786	Remote Similarity	NPD7825	Clinical (unspecified phase)
0.6786	Remote Similarity	NPD3100	Discontinued
0.6786	Remote Similarity	NPD4374	Clinical (unspecified phase)
0.6786	Remote Similarity	NPD8321	Discontinued
0.6784	Remote Similarity	NPD6803	Clinical (unspecified phase)
0.6784	Remote Similarity	NPD6957	Approved
0.6784	Remote Similarity	NPD6958	Approved
0.678	Remote Similarity	NPD3610	Approved
0.678	Remote Similarity	NPD3609	Approved
0.6777	Remote Similarity	NPD7424	Clinical (unspecified phase)
0.6776	Remote Similarity	NPD5913	Phase 3
0.6776	Remote Similarity	NPD5912	Clinical (unspecified phase)
0.6769	Remote Similarity	NPD3402	Phase 1
0.6769	Remote Similarity	NPD4555	Clinical (unspecified phase)
0.6768	Remote Similarity	NPD2012	Clinical (unspecified phase)
0.6765	Remote Similarity	NPD2640	Approved
0.6765	Remote Similarity	NPD2641	Approved
0.6765	Remote Similarity	NPD2185	Clinical (unspecified phase)
0.6762	Remote Similarity	NPD2391	Clinical (unspecified phase)
0.6759	Remote Similarity	NPD4602	Approved
0.6751	Remote Similarity	NPD6970	Phase 2
0.6748	Remote Similarity	NPD750	Phase 2
0.674	Remote Similarity	NPD7971	Clinical (unspecified phase)
0.674	Remote Similarity	NPD7970	Approved
0.6735	Remote Similarity	NPD1661	Suspended
0.6733	Remote Similarity	NPD8026	Phase 1
0.6728	Remote Similarity	NPD2960	Clinical (unspecified phase)
0.6727	Remote Similarity	NPD8629	Discontinued
0.6719	Remote Similarity	NPD786	Approved
0.6717	Remote Similarity	NPD2882	Phase 1
0.6716	Remote Similarity	NPD425	Approved
0.6716	Remote Similarity	NPD424	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