NPASS Compound

Structure

NPC251936 OpenBabel07101719132D 41 48 0 0 1 0 0 0 0 0999 V2000 -4.9279 -2.4595 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7470 0.5860 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2096 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2577 0.2377 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1721 -3.1144 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1357 0.6781 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9279 -0.5405 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5668 -0.2976 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9235 -1.1264 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5168 -0.2128 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1823 -3.2567 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5450 0.4959 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1721 0.1144 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6130 -0.9140 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3357 -1.9354 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5223 -0.1083 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2345 -1.6167 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2727 -2.8413 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0919 0.0754 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1823 0.2567 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3872 -1.4895 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1549 -1.3541 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3433 -2.0921 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3412 -1.8309 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -2.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.9345 -0.9173 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -2.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.7321 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -1.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.7321 -1.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.7321 -2.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8660 -0.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8660 -3.5000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -2.2727 -0.1587 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1.9400 -1.0219 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -2.9340 -1.9099 0.0000 N 0 0 3 0 0 0 0 0 0 0 0 0 -0.0000 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 3 1 0 0 0 0 1 5 2 0 0 0 0 2 4 1 0 0 0 0 2 6 2 0 0 0 0 3 7 1 0 0 0 0 4 8 1 0 0 0 0 5 11 1 0 0 0 0 6 12 1 0 0 0 0 7 13 1 0 0 0 0 8 14 1 0 0 0 0 9 10 2 0 0 0 0 9 15 1 0 0 0 0 10 16 1 0 0 0 0 11 19 1 0 0 0 0 12 20 1 0 0 0 0 13 21 1 0 0 0 0 14 23 1 0 0 0 0 15 26 2 0 0 0 0 16 29 2 0 0 0 0 17 22 2 0 0 0 0 17 27 1 0 0 0 0 18 24 1 0 0 0 0 18 28 1 0 0 0 0 21 38 1 0 0 0 0 22 37 1 0 0 0 0 23 40 1 0 0 0 0 24 40 1 0 0 0 0 25 35 1 0 0 0 0 25 40 1 0 0 0 0 26 27 1 0 0 0 0 26 29 1 0 0 0 0 27 31 2 0 0 0 0 28 30 1 0 0 0 0 28 35 1 1 0 0 0 29 39 1 0 0 0 0 30 32 1 1 0 0 0 30 33 1 0 0 0 0 31 32 1 0 0 0 0 31 39 1 0 0 0 0 32 37 2 0 0 0 0 33 36 1 6 0 0 0 33 41 1 0 0 0 0 34 35 1 1 0 0 0 34 36 1 0 0 0 0 34 38 1 0 0 0 0 35 19 1 1 0 0 0 36 20 1 6 0 0 0 36 41 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	550.37
Volume:	594.446
LogP:	4.528
LogD:	4.011
LogS:	-1.969
# Rotatable Bonds:	1
TPSA:	56.48
# H-Bond Aceptor:	5
# H-Bond Donor:	2
# Rings:	8
# Heavy Atoms:	5

MedChem Properties

QED Drug-Likeness Score:	0.247
Synthetic Accessibility Score:	7.042
Fsp3:	0.583
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:	-5.122
MDCK Permeability:	2.9117190933902748e-05
Pgp-inhibitor:	0.182
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.17
20% Bioavailability (F20%):	1.0
30% Bioavailability (F30%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.453
Plasma Protein Binding (PPB):	94.1939468383789%
Volume Distribution (VD):	3.427
Pgp-substrate:	4.9803009033203125%

ADMET: Metabolism

CYP1A2-inhibitor:	0.101
CYP1A2-substrate:	0.786
CYP2C19-inhibitor:	0.132
CYP2C19-substrate:	0.306
CYP2C9-inhibitor:	0.048
CYP2C9-substrate:	0.099
CYP2D6-inhibitor:	0.988
CYP2D6-substrate:	0.959
CYP3A4-inhibitor:	0.85
CYP3A4-substrate:	0.427

ADMET: Excretion

Clearance (CL):	3.721
Half-life (T1/2):	0.614

ADMET: Toxicity

hERG Blockers:	0.962
Human Hepatotoxicity (H-HT):	0.954
Drug-inuced Liver Injury (DILI):	0.076
AMES Toxicity:	0.204
Rat Oral Acute Toxicity:	0.77
Maximum Recommended Daily Dose:	0.965
Skin Sensitization:	0.967
Carcinogencity:	0.085
Eye Corrosion:	0.003
Eye Irritation:	0.007
Respiratory Toxicity:	0.963

Download Data

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

Natural Product: NPC251936

Natural Product ID:	NPC251936
*Common Name:**	Manzamine B
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	VLWWSOADVQPMJO-ZOSDTVTQSA-N
Standard InCHI:	InChI=1S/C36H46N4O/c1-3-7-13-21-38-34-35(19-11-5-1)25-40-23-14-8-4-2-6-12-20-36(34)33(41-36)30(28(35)18-24-40)32-31-27(17-22-37-32)26-15-9-10-16-29(26)39-31/h1-2,5-6,9-10,15-17,22,28,30,33-34,38-39H,3-4,7-8,11-14,18-21,23-25H2/b5-1-,6-2-/t28-,30+,33-,34+,35-,36-/m0/s1
SMILES:	C1CCCN[C@@H]2[C@@]3(CC/C=C1)CN1CCCC/C=CCC[C@]42O[C@H]4[C@H]([C@@H]3CC1)c1nccc2c1[nH]c1c2cccc1
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL507145
PubChem CID:	9937450
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.	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.	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.	n.a.	n.a.	PMID[28452477]

☑ 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	3

Activity Type	# Activity
Cell Line	3

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT139	Cell Line	HT-29	Homo sapiens	IC50	=	1.6	ug.mL-1	PMID[465631]
NPT81	Cell Line	A549	Homo sapiens	IC50	=	4.5	ug.mL-1	PMID[465631]
NPT168	Cell Line	P388	Mus musculus	IC50	=	6.6	ug.mL-1	PMID[465631]

☑ 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 NPC251936 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	650
0.1-0.2	3137
0.2-0.3	16482
0.3-0.4	15209
0.4-0.5	3278
0.5-0.6	2033
0.6-0.7	1671
0.7-0.8	229
0.8-0.85	3
0.85-0.9	1
0.9-0.95	1
0.95-1	3

Similarity Score	Similarity Level	Natural Product ID
0.8544	High Similarity	NPC472027
0.8485	Intermediate Similarity	NPC265576
0.8447	Intermediate Similarity	NPC473757
0.8341	Intermediate Similarity	NPC471506
0.8333	Intermediate Similarity	NPC473362
0.8333	Intermediate Similarity	NPC166492
0.8233	Intermediate Similarity	NPC476492
0.8195	Intermediate Similarity	NPC475288
0.8131	Intermediate Similarity	NPC95783
0.8065	Intermediate Similarity	NPC475258
0.8057	Intermediate Similarity	NPC250835
0.8018	Intermediate Similarity	NPC475338
0.8018	Intermediate Similarity	NPC909
0.7991	Intermediate Similarity	NPC81175
0.7982	Intermediate Similarity	NPC6215
0.7974	Intermediate Similarity	NPC471891
0.7944	Intermediate Similarity	NPC473310
0.7925	Intermediate Similarity	NPC475602
0.7873	Intermediate Similarity	NPC476451
0.7867	Intermediate Similarity	NPC126066
0.7828	Intermediate Similarity	NPC19679
0.7817	Intermediate Similarity	NPC300688
0.7773	Intermediate Similarity	NPC87755
0.775	Intermediate Similarity	NPC15102
0.7716	Intermediate Similarity	NPC151939
0.7706	Intermediate Similarity	NPC471564
0.77	Intermediate Similarity	NPC284678
0.77	Intermediate Similarity	NPC475422
0.7665	Intermediate Similarity	NPC41679
0.7619	Intermediate Similarity	NPC193761
0.7617	Intermediate Similarity	NPC5145
0.7612	Intermediate Similarity	NPC472294
0.7607	Intermediate Similarity	NPC476493
0.7606	Intermediate Similarity	NPC314957
0.759	Intermediate Similarity	NPC317430
0.7578	Intermediate Similarity	NPC476491
0.7565	Intermediate Similarity	NPC473312
0.7562	Intermediate Similarity	NPC472108
0.7562	Intermediate Similarity	NPC139291
0.7562	Intermediate Similarity	NPC48938
0.7547	Intermediate Similarity	NPC475070
0.7535	Intermediate Similarity	NPC123976
0.7535	Intermediate Similarity	NPC167860
0.7522	Intermediate Similarity	NPC469554
0.75	Intermediate Similarity	NPC201700
0.7489	Intermediate Similarity	NPC70155
0.7489	Intermediate Similarity	NPC304926
0.7489	Intermediate Similarity	NPC476041
0.7478	Intermediate Similarity	NPC477861
0.7475	Intermediate Similarity	NPC472110
0.7475	Intermediate Similarity	NPC472123
0.7475	Intermediate Similarity	NPC472109
0.7467	Intermediate Similarity	NPC314954
0.7464	Intermediate Similarity	NPC229332
0.7455	Intermediate Similarity	NPC281049
0.7437	Intermediate Similarity	NPC329688
0.7437	Intermediate Similarity	NPC189812
0.7411	Intermediate Similarity	NPC63751
0.7411	Intermediate Similarity	NPC313884
0.7411	Intermediate Similarity	NPC98371
0.7404	Intermediate Similarity	NPC474177
0.74	Intermediate Similarity	NPC280852
0.7397	Intermediate Similarity	NPC478157
0.7387	Intermediate Similarity	NPC314603
0.7385	Intermediate Similarity	NPC475778
0.7383	Intermediate Similarity	NPC470500
0.7379	Intermediate Similarity	NPC173028
0.7379	Intermediate Similarity	NPC65215
0.7373	Intermediate Similarity	NPC234999
0.7371	Intermediate Similarity	NPC56765
0.7371	Intermediate Similarity	NPC162730
0.7371	Intermediate Similarity	NPC474116
0.7371	Intermediate Similarity	NPC476874
0.7368	Intermediate Similarity	NPC133366
0.7368	Intermediate Similarity	NPC101543
0.7366	Intermediate Similarity	NPC266192
0.7363	Intermediate Similarity	NPC68354
0.7363	Intermediate Similarity	NPC59269
0.736	Intermediate Similarity	NPC160105
0.7358	Intermediate Similarity	NPC79129
0.7358	Intermediate Similarity	NPC249150
0.7358	Intermediate Similarity	NPC313985
0.7358	Intermediate Similarity	NPC49196
0.7358	Intermediate Similarity	NPC195461
0.7358	Intermediate Similarity	NPC81654
0.7352	Intermediate Similarity	NPC221100
0.7352	Intermediate Similarity	NPC234078
0.735	Intermediate Similarity	NPC275305
0.735	Intermediate Similarity	NPC37423
0.7347	Intermediate Similarity	NPC311276
0.7346	Intermediate Similarity	NPC50503
0.7344	Intermediate Similarity	NPC325903
0.7342	Intermediate Similarity	NPC193267
0.7342	Intermediate Similarity	NPC213530
0.7333	Intermediate Similarity	NPC255229
0.7333	Intermediate Similarity	NPC81229
0.733	Intermediate Similarity	NPC317030
0.733	Intermediate Similarity	NPC204565
0.7327	Intermediate Similarity	NPC478158
0.7327	Intermediate Similarity	NPC133261
0.7327	Intermediate Similarity	NPC141377
0.7324	Intermediate Similarity	NPC232727
0.7323	Intermediate Similarity	NPC154293
0.7302	Intermediate Similarity	NPC470505
0.7301	Intermediate Similarity	NPC267926
0.7299	Intermediate Similarity	NPC232130
0.7286	Intermediate Similarity	NPC194411
0.7282	Intermediate Similarity	NPC230869
0.7282	Intermediate Similarity	NPC474707
0.7277	Intermediate Similarity	NPC176538
0.7277	Intermediate Similarity	NPC303820
0.7277	Intermediate Similarity	NPC106771
0.7277	Intermediate Similarity	NPC205254
0.7277	Intermediate Similarity	NPC23420
0.7273	Intermediate Similarity	NPC324149
0.7273	Intermediate Similarity	NPC295228
0.7273	Intermediate Similarity	NPC49954
0.7273	Intermediate Similarity	NPC474561
0.7269	Intermediate Similarity	NPC57690
0.726	Intermediate Similarity	NPC208284
0.7256	Intermediate Similarity	NPC476138
0.7256	Intermediate Similarity	NPC245816
0.7256	Intermediate Similarity	NPC477135
0.7255	Intermediate Similarity	NPC314394
0.7255	Intermediate Similarity	NPC233936
0.7244	Intermediate Similarity	NPC155444
0.7243	Intermediate Similarity	NPC52909
0.7243	Intermediate Similarity	NPC475506
0.7243	Intermediate Similarity	NPC94211
0.7243	Intermediate Similarity	NPC475935
0.7241	Intermediate Similarity	NPC215795
0.7241	Intermediate Similarity	NPC176199
0.7237	Intermediate Similarity	NPC253580
0.7228	Intermediate Similarity	NPC24594
0.7228	Intermediate Similarity	NPC203754
0.7228	Intermediate Similarity	NPC150048
0.7228	Intermediate Similarity	NPC472122
0.7227	Intermediate Similarity	NPC26679
0.7225	Intermediate Similarity	NPC24370
0.7225	Intermediate Similarity	NPC469811
0.7225	Intermediate Similarity	NPC319232
0.7222	Intermediate Similarity	NPC285558
0.722	Intermediate Similarity	NPC477714
0.7209	Intermediate Similarity	NPC155143
0.7207	Intermediate Similarity	NPC183407
0.7207	Intermediate Similarity	NPC204491
0.7207	Intermediate Similarity	NPC203614
0.7205	Intermediate Similarity	NPC477175
0.7205	Intermediate Similarity	NPC470730
0.7198	Intermediate Similarity	NPC94752
0.7196	Intermediate Similarity	NPC19872
0.7194	Intermediate Similarity	NPC206819
0.7194	Intermediate Similarity	NPC41257
0.7194	Intermediate Similarity	NPC318065
0.7193	Intermediate Similarity	NPC470126
0.719	Intermediate Similarity	NPC472113
0.7188	Intermediate Similarity	NPC321911
0.7186	Intermediate Similarity	NPC54988
0.7184	Intermediate Similarity	NPC165201
0.7183	Intermediate Similarity	NPC192315
0.7183	Intermediate Similarity	NPC473640
0.7179	Intermediate Similarity	NPC469785
0.7177	Intermediate Similarity	NPC329858
0.7177	Intermediate Similarity	NPC469470
0.7177	Intermediate Similarity	NPC472112
0.7177	Intermediate Similarity	NPC469501
0.7175	Intermediate Similarity	NPC477715
0.7174	Intermediate Similarity	NPC475969
0.7174	Intermediate Similarity	NPC475859
0.7174	Intermediate Similarity	NPC290529
0.7173	Intermediate Similarity	NPC63545
0.7172	Intermediate Similarity	NPC317105
0.717	Intermediate Similarity	NPC205403
0.7162	Intermediate Similarity	NPC56109
0.7162	Intermediate Similarity	NPC191382
0.7157	Intermediate Similarity	NPC279918
0.7156	Intermediate Similarity	NPC477065
0.715	Intermediate Similarity	NPC188387
0.715	Intermediate Similarity	NPC62510
0.715	Intermediate Similarity	NPC476167
0.715	Intermediate Similarity	NPC476319
0.715	Intermediate Similarity	NPC100321
0.715	Intermediate Similarity	NPC163421
0.7143	Intermediate Similarity	NPC286427
0.7143	Intermediate Similarity	NPC469762
0.7143	Intermediate Similarity	NPC165743
0.7137	Intermediate Similarity	NPC64216
0.7135	Intermediate Similarity	NPC179787
0.7135	Intermediate Similarity	NPC201380
0.713	Intermediate Similarity	NPC473761
0.7129	Intermediate Similarity	NPC213629
0.7128	Intermediate Similarity	NPC80597
0.7128	Intermediate Similarity	NPC75540
0.7128	Intermediate Similarity	NPC212376
0.7128	Intermediate Similarity	NPC70922
0.7128	Intermediate Similarity	NPC211572
0.7124	Intermediate Similarity	NPC310118
0.7122	Intermediate Similarity	NPC187827
0.7122	Intermediate Similarity	NPC472105
0.7121	Intermediate Similarity	NPC470203

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 NPC251936 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	293
0.1-0.2	566
0.2-0.3	1013
0.3-0.4	2057
0.4-0.5	2614
0.5-0.6	1899
0.6-0.7	656
0.7-0.8	52
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
0.799	Intermediate Similarity	NPD2125	Clinical (unspecified phase)
0.7668	Intermediate Similarity	NPD7824	Approved
0.7662	Intermediate Similarity	NPD6610	Clinical (unspecified phase)
0.7578	Intermediate Similarity	NPD7730	Approved
0.7578	Intermediate Similarity	NPD7731	Approved
0.7568	Intermediate Similarity	NPD7271	Approved
0.7512	Intermediate Similarity	NPD7958	Clinical (unspecified phase)
0.7512	Intermediate Similarity	NPD7957	Phase 1
0.75	Intermediate Similarity	NPD8431	Approved
0.7489	Intermediate Similarity	NPD7953	Approved
0.7489	Intermediate Similarity	NPD7791	Approved
0.7489	Intermediate Similarity	NPD7951	Approved
0.7489	Intermediate Similarity	NPD7790	Approved
0.7489	Intermediate Similarity	NPD7952	Approved
0.7489	Intermediate Similarity	NPD7950	Approved
0.7489	Intermediate Similarity	NPD7789	Approved
0.7487	Intermediate Similarity	NPD6375	Clinical (unspecified phase)
0.7476	Intermediate Similarity	NPD5912	Clinical (unspecified phase)
0.7476	Intermediate Similarity	NPD5913	Phase 3
0.7442	Intermediate Similarity	NPD7947	Clinical (unspecified phase)
0.7437	Intermediate Similarity	NPD5065	Approved
0.7436	Intermediate Similarity	NPD3323	Discontinued
0.7413	Intermediate Similarity	NPD4076	Approved
0.7413	Intermediate Similarity	NPD4079	Approved
0.7411	Intermediate Similarity	NPD6976	Clinical (unspecified phase)
0.7409	Intermediate Similarity	NPD7823	Clinical (unspecified phase)
0.7385	Intermediate Similarity	NPD3330	Phase 1
0.7363	Intermediate Similarity	NPD6203	Clinical (unspecified phase)
0.7363	Intermediate Similarity	NPD4181	Approved
0.7363	Intermediate Similarity	NPD3506	Approved
0.7363	Intermediate Similarity	NPD3505	Approved
0.7358	Intermediate Similarity	NPD4601	Approved
0.7358	Intermediate Similarity	NPD4600	Approved
0.7345	Intermediate Similarity	NPD6978	Phase 2
0.7345	Intermediate Similarity	NPD6977	Clinical (unspecified phase)
0.7342	Intermediate Similarity	NPD3402	Phase 1
0.7315	Intermediate Similarity	NPD6838	Clinical (unspecified phase)
0.7311	Intermediate Similarity	NPD6661	Clinical (unspecified phase)
0.731	Intermediate Similarity	NPD5744	Clinical (unspecified phase)
0.7306	Intermediate Similarity	NPD7594	Clinical (unspecified phase)
0.7295	Intermediate Similarity	NPD8110	Clinical (unspecified phase)
0.7291	Intermediate Similarity	NPD6595	Phase 3
0.7273	Intermediate Similarity	NPD5891	Approved
0.7246	Intermediate Similarity	NPD8021	Approved
0.7246	Intermediate Similarity	NPD8020	Approved
0.7246	Intermediate Similarity	NPD3486	Clinical (unspecified phase)
0.7246	Intermediate Similarity	NPD3961	Discontinued
0.724	Intermediate Similarity	NPD8112	Clinical (unspecified phase)
0.7236	Intermediate Similarity	NPD4779	Clinical (unspecified phase)
0.7236	Intermediate Similarity	NPD5862	Discovery
0.7235	Intermediate Similarity	NPD8410	Clinical (unspecified phase)
0.7217	Intermediate Similarity	NPD7948	Phase 1
0.7206	Intermediate Similarity	NPD6277	Clinical (unspecified phase)
0.72	Intermediate Similarity	NPD4184	Clinical (unspecified phase)
0.7192	Intermediate Similarity	NPD2144	Approved
0.7177	Intermediate Similarity	NPD6281	Approved
0.7171	Intermediate Similarity	NPD3038	Discontinued
0.7165	Intermediate Similarity	NPD2837	Discontinued
0.7164	Intermediate Similarity	NPD5934	Clinical (unspecified phase)
0.7162	Intermediate Similarity	NPD7781	Approved
0.7162	Intermediate Similarity	NPD7780	Approved
0.713	Intermediate Similarity	NPD5721	Clinical (unspecified phase)
0.7124	Intermediate Similarity	NPD6615	Clinical (unspecified phase)
0.7117	Intermediate Similarity	NPD8488	Clinical (unspecified phase)
0.7112	Intermediate Similarity	NPD7558	Phase 2
0.7109	Intermediate Similarity	NPD3404	Approved
0.7097	Intermediate Similarity	NPD4886	Phase 2
0.7095	Intermediate Similarity	NPD8063	Discontinued
0.7094	Intermediate Similarity	NPD4128	Approved
0.7089	Intermediate Similarity	NPD4440	Clinical (unspecified phase)
0.7087	Intermediate Similarity	NPD5559	Phase 2
0.7085	Intermediate Similarity	NPD7073	Clinical (unspecified phase)
0.7079	Intermediate Similarity	NPD3610	Approved
0.7079	Intermediate Similarity	NPD3609	Approved
0.7075	Intermediate Similarity	NPD5575	Clinical (unspecified phase)
0.7074	Intermediate Similarity	NPD6352	Phase 2
0.7072	Intermediate Similarity	NPD8093	Discontinued
0.7072	Intermediate Similarity	NPD8458	Clinical (unspecified phase)
0.7067	Intermediate Similarity	NPD7424	Clinical (unspecified phase)
0.7065	Intermediate Similarity	NPD5069	Clinical (unspecified phase)
0.7064	Intermediate Similarity	NPD5426	Phase 3
0.7064	Intermediate Similarity	NPD4795	Phase 2
0.7059	Intermediate Similarity	NPD4075	Phase 2
0.7054	Intermediate Similarity	NPD3394	Approved
0.7054	Intermediate Similarity	NPD3389	Approved
0.7054	Intermediate Similarity	NPD3393	Approved
0.7053	Intermediate Similarity	NPD5728	Clinical (unspecified phase)
0.7024	Intermediate Similarity	NPD8123	Approved
0.7024	Intermediate Similarity	NPD8122	Approved
0.7023	Intermediate Similarity	NPD7889	Clinical (unspecified phase)
0.7022	Intermediate Similarity	NPD8406	Clinical (unspecified phase)
0.7018	Intermediate Similarity	NPD8072	Approved
0.7014	Intermediate Similarity	NPD4499	Approved
0.7005	Intermediate Similarity	NPD8408	Discontinued
0.7	Intermediate Similarity	NPD8493	Clinical (unspecified phase)
0.6991	Remote Similarity	NPD4118	Clinical (unspecified phase)
0.6991	Remote Similarity	NPD8405	Clinical (unspecified phase)
0.6991	Remote Similarity	NPD7621	Clinical (unspecified phase)
0.699	Remote Similarity	NPD8386	Phase 2
0.6986	Remote Similarity	NPD8272	Phase 2
0.698	Remote Similarity	NPD4640	Approved
0.698	Remote Similarity	NPD4639	Approved
0.698	Remote Similarity	NPD4638	Approved
0.6974	Remote Similarity	NPD7726	Phase 1
0.6972	Remote Similarity	NPD8073	Approved
0.6967	Remote Similarity	NPD8442	Discontinued
0.6963	Remote Similarity	NPD7618	Phase 3
0.6963	Remote Similarity	NPD1722	Approved
0.6963	Remote Similarity	NPD7619	Phase 3
0.6962	Remote Similarity	NPD2921	Clinical (unspecified phase)
0.696	Remote Similarity	NPD4555	Clinical (unspecified phase)
0.6957	Remote Similarity	NPD8464	Clinical (unspecified phase)
0.6955	Remote Similarity	NPD4862	Clinical (unspecified phase)
0.6951	Remote Similarity	NPD7470	Discontinued
0.695	Remote Similarity	NPD1853	Clinical (unspecified phase)
0.6946	Remote Similarity	NPD1325	Approved
0.6946	Remote Similarity	NPD1326	Approved
0.6941	Remote Similarity	NPD2121	Clinical (unspecified phase)
0.6926	Remote Similarity	NPD8289	Discontinued
0.6923	Remote Similarity	NPD4374	Clinical (unspecified phase)
0.6914	Remote Similarity	NPD6503	Clinical (unspecified phase)
0.6909	Remote Similarity	NPD7712	Clinical (unspecified phase)
0.6906	Remote Similarity	NPD3014	Clinical (unspecified phase)
0.6906	Remote Similarity	NPD7809	Clinical (unspecified phase)
0.6906	Remote Similarity	NPD3013	Phase 3
0.6903	Remote Similarity	NPD5612	Discontinued
0.6898	Remote Similarity	NPD6664	Approved
0.6893	Remote Similarity	NPD2380	Approved
0.6893	Remote Similarity	NPD2381	Approved
0.6893	Remote Similarity	NPD2382	Approved
0.689	Remote Similarity	NPD5596	Phase 2
0.6889	Remote Similarity	NPD8094	Discontinued
0.6886	Remote Similarity	NPD7194	Discontinued
0.6884	Remote Similarity	NPD7944	Discontinued
0.6881	Remote Similarity	NPD1740	Approved
0.6881	Remote Similarity	NPD1739	Approved
0.6881	Remote Similarity	NPD4500	Approved
0.6881	Remote Similarity	NPD4501	Approved
0.6878	Remote Similarity	NPD4023	Clinical (unspecified phase)
0.6878	Remote Similarity	NPD4112	Clinical (unspecified phase)
0.6872	Remote Similarity	NPD4703	Approved
0.6872	Remote Similarity	NPD4702	Approved
0.6872	Remote Similarity	NPD4547	Phase 3
0.6858	Remote Similarity	NPD6140	Clinical (unspecified phase)
0.6857	Remote Similarity	NPD6178	Phase 3
0.6853	Remote Similarity	NPD7675	Phase 3
0.6853	Remote Similarity	NPD7676	Clinical (unspecified phase)
0.6853	Remote Similarity	NPD7674	Phase 3
0.6853	Remote Similarity	NPD7603	Discontinued
0.6849	Remote Similarity	NPD8629	Discontinued
0.6847	Remote Similarity	NPD8322	Phase 2
0.6847	Remote Similarity	NPD1392	Approved
0.6846	Remote Similarity	NPD5483	Clinical (unspecified phase)
0.6844	Remote Similarity	NPD7455	Approved
0.6844	Remote Similarity	NPD7454	Approved
0.6842	Remote Similarity	NPD8109	Clinical (unspecified phase)
0.6842	Remote Similarity	NPD7867	Phase 1
0.684	Remote Similarity	NPD5590	Clinical (unspecified phase)
0.684	Remote Similarity	NPD7394	Phase 2
0.6839	Remote Similarity	NPD4637	Clinical (unspecified phase)
0.6838	Remote Similarity	NPD6968	Phase 2
0.6838	Remote Similarity	NPD6969	Phase 2
0.6837	Remote Similarity	NPD3100	Discontinued
0.6837	Remote Similarity	NPD802	Phase 2
0.6837	Remote Similarity	NPD1304	Clinical (unspecified phase)
0.6835	Remote Similarity	NPD3825	Phase 3
0.6832	Remote Similarity	NPD6635	Approved
0.683	Remote Similarity	NPD7998	Clinical (unspecified phase)
0.683	Remote Similarity	NPD8321	Discontinued
0.6825	Remote Similarity	NPD6227	Discontinued
0.6822	Remote Similarity	NPD6630	Clinical (unspecified phase)
0.682	Remote Similarity	NPD6992	Phase 2
0.6816	Remote Similarity	NPD2510	Approved
0.6816	Remote Similarity	NPD7665	Phase 2
0.6816	Remote Similarity	NPD7666	Phase 3
0.6816	Remote Similarity	NPD5658	Approved
0.6816	Remote Similarity	NPD2509	Approved
0.681	Remote Similarity	NPD2094	Phase 2
0.681	Remote Similarity	NPD2095	Phase 2
0.681	Remote Similarity	NPD2092	Phase 2
0.6808	Remote Similarity	NPD7233	Approved
0.6808	Remote Similarity	NPD7234	Approved
0.6803	Remote Similarity	NPD5482	Discontinued
0.6802	Remote Similarity	NPD2172	Phase 1
0.6802	Remote Similarity	NPD7001	Phase 3
0.6802	Remote Similarity	NPD3003	Approved
0.68	Remote Similarity	NPD2581	Approved
0.68	Remote Similarity	NPD2582	Approved
0.6798	Remote Similarity	NPD7423	Phase 2
0.6792	Remote Similarity	NPD3378	Clinical (unspecified phase)
0.6792	Remote Similarity	NPD706	Phase 1
0.679	Remote Similarity	NPD8358	Approved
0.6786	Remote Similarity	NPD6545	Clinical (unspecified phase)
0.6784	Remote Similarity	NPD975	Approved
0.6784	Remote Similarity	NPD976	Approved
0.6784	Remote Similarity	NPD977	Approved
0.6783	Remote Similarity	NPD6717	Clinical (unspecified phase)
0.6777	Remote Similarity	NPD4957	Phase 2
0.6777	Remote Similarity	NPD2091	Phase 2
0.6777	Remote Similarity	NPD2096	Phase 2

Bioactivity similarity: Similar Natural Products in NPASS

Bioactivity similarity was calculated based on bioactivity descriptors of compounds. The bioactivity descriptors were calculated by a recently developed AI algorithm Chemical Checker (CC) [Nature Biotechnology, 38:1087–1096, 2020; Nature Communications, 12:3932, 2021], which evaluated bioactivity similarities at five levels:
☉ A: chemistry similarity;
☉ B: biological targets similarity;
☉ C: networks similarity;
☉ D: cell-based bioactivity similarity;
☉ E: similarity based on clinical data.

Those 5 categories of CC bioactivity descriptors were calculated and then subjected to manifold projection using UMAP algorithm, to project all NPs on a 2-Dimensional space. The current NP was highlighted with a small circle in the 2-D map. Below figures: left-to-right, A-to-E.

A: chemistry similarity

B: biological targets similarity

C: networks similarity

D: cell-based bioactivity similarity

E: similarity based on clinical data