NPASS Compound

Structure

NPC304499 OpenBabel07101719252D 32 35 0 0 1 0 0 0 0 0999 V2000 -4.7515 2.4328 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0387 3.5917 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4570 3.5032 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4593 2.4135 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1042 2.9680 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4133 3.9190 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4049 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0605 3.3838 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1261 2.7601 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.4641 -1.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.8171 1.8090 0.0000 C 0 0 2 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 -4.3914 4.1270 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.8171 0.1910 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8660 -1.5000 0.0000 C 0 0 1 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 0.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.7321 0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8660 1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.3301 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.7004 5.0780 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.1261 -0.7601 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 15 1 0 0 0 0 2 15 1 0 0 0 0 6 7 1 0 0 0 0 6 16 1 0 0 0 0 7 20 1 0 0 0 0 8 10 1 0 0 0 0 8 17 1 0 0 0 0 9 11 1 0 0 0 0 9 23 1 0 0 0 0 10 25 1 0 0 0 0 11 26 1 0 0 0 0 12 17 1 0 0 0 0 12 19 1 0 0 0 0 13 18 1 0 0 0 0 13 21 1 0 0 0 0 14 22 1 0 0 0 0 14 27 1 0 0 0 0 15 20 1 0 0 0 0 16 3 1 1 0 0 0 16 18 1 0 0 0 0 17 28 1 6 0 0 0 18 26 1 6 0 0 0 19 22 1 0 0 0 0 19 25 1 6 0 0 0 20 29 1 1 0 0 0 21 24 1 0 0 0 0 21 30 1 6 0 0 0 22 31 1 1 0 0 0 23 25 1 6 0 0 0 23 27 1 0 0 0 0 24 26 1 6 0 0 0 24 27 1 0 0 0 0 25 4 1 6 0 0 0 26 5 1 6 0 0 0 27 32 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	452.35
Volume:	485.273
LogP:	3.778
LogD:	3.94
LogS:	-3.904
# Rotatable Bonds:	5
TPSA:	101.15
# H-Bond Aceptor:	5
# H-Bond Donor:	5
# Rings:	4
# Heavy Atoms:	5

MedChem Properties

QED Drug-Likeness Score:	0.44
Synthetic Accessibility Score:	5.007
Fsp3:	1.0
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:	-4.891
MDCK Permeability:	2.7311351004755124e-05
Pgp-inhibitor:	0.324
Pgp-substrate:	0.998
Human Intestinal Absorption (HIA):	0.01
20% Bioavailability (F20%):	0.467
30% Bioavailability (F30%):	0.429

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.168
Plasma Protein Binding (PPB):	88.81793975830078%
Volume Distribution (VD):	0.845
Pgp-substrate:	5.945133209228516%

ADMET: Metabolism

CYP1A2-inhibitor:	0.011
CYP1A2-substrate:	0.606
CYP2C19-inhibitor:	0.005
CYP2C19-substrate:	0.812
CYP2C9-inhibitor:	0.033
CYP2C9-substrate:	0.074
CYP2D6-inhibitor:	0.001
CYP2D6-substrate:	0.082
CYP3A4-inhibitor:	0.24
CYP3A4-substrate:	0.253

ADMET: Excretion

Clearance (CL):	7.42
Half-life (T1/2):	0.193

ADMET: Toxicity

hERG Blockers:	0.168
Human Hepatotoxicity (H-HT):	0.317
Drug-inuced Liver Injury (DILI):	0.024
AMES Toxicity:	0.008
Rat Oral Acute Toxicity:	0.04
Maximum Recommended Daily Dose:	0.313
Skin Sensitization:	0.904
Carcinogencity:	0.156
Eye Corrosion:	0.566
Eye Irritation:	0.121
Respiratory Toxicity:	0.975

Download Data

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

Natural Product: NPC304499

Natural Product ID:	NPC304499
*Common Name:**	(3S,5S,6S,8S,9R,10S,13R,14S,15R,17R)-17-((2R,5S)-5-Hydroxy-6-Methylheptan-2-Yl)-10,13-Dimethylhexadecahydro-1H-Cyclopenta[A]Phenanthrene-3,6,8,15-Tetraol
IUPAC Name:	(3S,5S,6S,8S,9R,10S,13R,14S,15R,17R)-17-[(2R,5S)-5-hydroxy-6-methylheptan-2-yl]-10,13-dimethyl-1,2,3,4,5,6,7,9,11,12,14,15,16,17-tetradecahydrocyclopenta[a]phenanthrene-3,6,8,15-tetrol
Synonyms:
Standard InCHIKey:	SOWQHVUKEGVMMG-SASNHPFXSA-N
Standard InCHI:	InChI=1S/C27H48O5/c1-15(2)20(29)7-6-16(3)18-13-21(30)24-26(18,5)11-9-23-25(4)10-8-17(28)12-19(25)22(31)14-27(23,24)32/h15-24,28-32H,6-14H2,1-5H3/t16-,17+,18-,19-,20+,21-,22+,23-,24-,25+,26-,27+/m1/s1
SMILES:	CC(C)[C@H](CC[C@@H](C)[C@H]1C[C@H]([C@@H]2[C@]1(C)CC[C@@H]1[C@@]3(C)CC[C@@H](C[C@@H]3[C@H](C[C@@]21O)O)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL516693
PubChem CID:	14680252
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0001445] Bile acids, alcohols and derivatives [CHEMONTID:0002194] Hydroxy bile acids, alcohols and derivatives [CHEMONTID:0001110] Tetrahydroxy bile acids, alcohols 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
NPO7293	Certonardoa semiregularis	Species	Ophidiasteridae	Eukaryota	n.a.	n.a.	n.a.	PMID[12444692]
NPO7293	Certonardoa semiregularis	Species	Ophidiasteridae	Eukaryota	n.a.	n.a.	n.a.	PMID[12662097]
NPO7293	Certonardoa semiregularis	Species	Ophidiasteridae	Eukaryota	n.a.	n.a.	n.a.	PMID[15104487]
NPO7293	Certonardoa semiregularis	Species	Ophidiasteridae	Eukaryota	n.a.	n.a.	n.a.	PMID[15497935]
NPO33455	nardoa tuberculata	Species	Ophidiasteridae	Eukaryota	n.a.	Okinawan, Japan	n.a.	PMID[8377014]

☑ 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	5
MIC	21

Activity Type	# Activity
Cell Line	5
Organism	21

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT81	Cell Line	A549	Homo sapiens	ED50	=	11.3	ug ml-1	PMID[479532]
NPT146	Cell Line	SK-OV-3	Homo sapiens	ED50	=	15.6	ug ml-1	PMID[479532]
NPT147	Cell Line	SK-MEL-2	Homo sapiens	ED50	=	12.4	ug ml-1	PMID[479532]
NPT574	Cell Line	XF498	Homo sapiens	ED50	=	11.4	ug ml-1	PMID[479532]
NPT148	Cell Line	HCT-15	Homo sapiens	ED50	=	19.4	ug ml-1	PMID[479532]
NPT1228	Organism	Streptococcus pyogenes	Streptococcus pyogenes	MIC	=	12.5	ug.mL-1	PMID[479532]
NPT1228	Organism	Streptococcus pyogenes	Streptococcus pyogenes	MIC	>	25.0	ug.mL-1	PMID[479532]
NPT18	Organism	Pseudomonas aeruginosa	Pseudomonas aeruginosa	MIC	>	25.0	ug.mL-1	PMID[479532]
NPT18	Organism	Pseudomonas aeruginosa	Pseudomonas aeruginosa	MIC	=	25.0	ug.mL-1	PMID[479532]
NPT1531	Organism	Enterococcus faecium	Enterococcus faecium	MIC	>	25.0	ug.mL-1	PMID[479532]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	>	25.0	ug.mL-1	PMID[479532]
NPT19	Organism	Escherichia coli	Escherichia coli	MIC	>	25.0	ug.mL-1	PMID[479532]
NPT566	Organism	Salmonella typhimurium	Salmonella enterica subsp. enterica serovar Typhimurium	MIC	>	25.0	ug.mL-1	PMID[479532]
NPT4997	Organism	Klebsiella oxytoca	Klebsiella oxytoca	MIC	>	25.0	ug.mL-1	PMID[479532]
NPT720	Organism	Enterobacter aerogenes	Enterobacter aerogenes	MIC	>	25.0	ug.mL-1	PMID[479532]
NPT1033	Organism	Enterobacter cloacae	Enterobacter cloacae	MIC	>	25.0	ug.mL-1	PMID[479532]
NPT985	Organism	Cladosporium cucumerinum	Cladosporium cucumerinum	MIC	=	3.0	ug	PMID[479533]

☑ 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 NPC304499 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	402
0.1-0.2	4469
0.2-0.3	14892
0.3-0.4	10275
0.4-0.5	4933
0.5-0.6	4413
0.6-0.7	2472
0.7-0.8	649
0.8-0.85	106
0.85-0.9	39
0.9-0.95	33
0.95-1	14

Similarity Score	Similarity Level	Natural Product ID
0.9577	High Similarity	NPC185915
0.9577	High Similarity	NPC477227
0.9577	High Similarity	NPC192046
0.9577	High Similarity	NPC302578
0.9577	High Similarity	NPC105208
0.9577	High Similarity	NPC128951
0.9571	High Similarity	NPC317242
0.9559	High Similarity	NPC232925
0.9559	High Similarity	NPC251201
0.9559	High Similarity	NPC63588
0.9444	High Similarity	NPC67657
0.9444	High Similarity	NPC18857
0.9437	High Similarity	NPC163597
0.9412	High Similarity	NPC66407
0.9412	High Similarity	NPC477820
0.9315	High Similarity	NPC287452
0.9296	High Similarity	NPC196136
0.9296	High Similarity	NPC158208
0.9296	High Similarity	NPC243027
0.9286	High Similarity	NPC470610
0.9286	High Similarity	NPC153719
0.9265	High Similarity	NPC474756
0.9155	High Similarity	NPC10476
0.9155	High Similarity	NPC475458
0.9155	High Similarity	NPC228994
0.9155	High Similarity	NPC192501
0.9155	High Similarity	NPC48795
0.9143	High Similarity	NPC127094
0.9143	High Similarity	NPC1340
0.9143	High Similarity	NPC470071
0.9143	High Similarity	NPC187471
0.9143	High Similarity	NPC252182
0.9041	High Similarity	NPC476233
0.9	High Similarity	NPC192192
0.8971	High Similarity	NPC44122
0.8919	High Similarity	NPC147993
0.8857	High Similarity	NPC129829
0.8857	High Similarity	NPC254037
0.8857	High Similarity	NPC107919
0.8831	High Similarity	NPC232023
0.8831	High Similarity	NPC478054
0.88	High Similarity	NPC477282
0.88	High Similarity	NPC269333
0.88	High Similarity	NPC81074
0.8714	High Similarity	NPC472741
0.8701	High Similarity	NPC475388
0.8676	High Similarity	NPC118937
0.8676	High Similarity	NPC281540
0.8676	High Similarity	NPC159654
0.8676	High Similarity	NPC167995
0.8667	High Similarity	NPC471045
0.8667	High Similarity	NPC471769
0.8611	High Similarity	NPC109457
0.8611	High Similarity	NPC100586
0.8611	High Similarity	NPC157422
0.8608	High Similarity	NPC266651
0.8592	High Similarity	NPC470833
0.8571	High Similarity	NPC48079
0.8571	High Similarity	NPC475884
0.8571	High Similarity	NPC473230
0.8571	High Similarity	NPC63190
0.8553	High Similarity	NPC476176
0.8533	High Similarity	NPC474574
0.8533	High Similarity	NPC64081
0.8533	High Similarity	NPC11907
0.8533	High Similarity	NPC133596
0.8529	High Similarity	NPC236099
0.8529	High Similarity	NPC209686
0.8529	High Similarity	NPC249078
0.8529	High Similarity	NPC114891
0.85	High Similarity	NPC121981
0.85	High Similarity	NPC201273
0.85	High Similarity	NPC6605
0.8472	Intermediate Similarity	NPC282454
0.8462	Intermediate Similarity	NPC202688
0.8462	Intermediate Similarity	NPC60018
0.8462	Intermediate Similarity	NPC154043
0.8442	Intermediate Similarity	NPC78545
0.8442	Intermediate Similarity	NPC71535
0.8442	Intermediate Similarity	NPC474714
0.8442	Intermediate Similarity	NPC16449
0.8429	Intermediate Similarity	NPC142712
0.8421	Intermediate Similarity	NPC31828
0.8421	Intermediate Similarity	NPC477819
0.8421	Intermediate Similarity	NPC477817
0.84	Intermediate Similarity	NPC470145
0.8382	Intermediate Similarity	NPC148174
0.8382	Intermediate Similarity	NPC218585
0.8382	Intermediate Similarity	NPC71460
0.8378	Intermediate Similarity	NPC477508
0.8356	Intermediate Similarity	NPC478103
0.8354	Intermediate Similarity	NPC85095
0.8354	Intermediate Similarity	NPC216420
0.8354	Intermediate Similarity	NPC211135
0.8333	Intermediate Similarity	NPC241085
0.8333	Intermediate Similarity	NPC469745
0.8333	Intermediate Similarity	NPC299948
0.8333	Intermediate Similarity	NPC470830
0.8286	Intermediate Similarity	NPC472946
0.8286	Intermediate Similarity	NPC475943
0.8286	Intermediate Similarity	NPC474380
0.8286	Intermediate Similarity	NPC41577
0.8286	Intermediate Similarity	NPC473276
0.8286	Intermediate Similarity	NPC190827
0.8286	Intermediate Similarity	NPC243469
0.8267	Intermediate Similarity	NPC139765
0.8267	Intermediate Similarity	NPC231680
0.8267	Intermediate Similarity	NPC270306
0.8267	Intermediate Similarity	NPC131584
0.8267	Intermediate Similarity	NPC91387
0.825	Intermediate Similarity	NPC256567
0.825	Intermediate Similarity	NPC320824
0.825	Intermediate Similarity	NPC255882
0.825	Intermediate Similarity	NPC50438
0.8228	Intermediate Similarity	NPC296734
0.8228	Intermediate Similarity	NPC470611
0.8219	Intermediate Similarity	NPC231945
0.8205	Intermediate Similarity	NPC475679
0.8194	Intermediate Similarity	NPC469987
0.8193	Intermediate Similarity	NPC109744
0.8171	Intermediate Similarity	NPC210658
0.8171	Intermediate Similarity	NPC161928
0.8158	Intermediate Similarity	NPC477602
0.8158	Intermediate Similarity	NPC473916
0.8158	Intermediate Similarity	NPC477601
0.8143	Intermediate Similarity	NPC69149
0.8133	Intermediate Similarity	NPC478130
0.8125	Intermediate Similarity	NPC193870
0.8125	Intermediate Similarity	NPC327451
0.8125	Intermediate Similarity	NPC110778
0.8125	Intermediate Similarity	NPC470929
0.8125	Intermediate Similarity	NPC141941
0.8108	Intermediate Similarity	NPC131506
0.8108	Intermediate Similarity	NPC473279
0.8108	Intermediate Similarity	NPC195530
0.8108	Intermediate Similarity	NPC157777
0.8101	Intermediate Similarity	NPC73515
0.8095	Intermediate Similarity	NPC475751
0.8095	Intermediate Similarity	NPC279329
0.8095	Intermediate Similarity	NPC473956
0.8082	Intermediate Similarity	NPC99264
0.8077	Intermediate Similarity	NPC220379
0.8077	Intermediate Similarity	NPC24504
0.8077	Intermediate Similarity	NPC476316
0.8077	Intermediate Similarity	NPC116119
0.8077	Intermediate Similarity	NPC472742
0.8077	Intermediate Similarity	NPC80297
0.8077	Intermediate Similarity	NPC475727
0.8072	Intermediate Similarity	NPC128475
0.8052	Intermediate Similarity	NPC212453
0.8049	Intermediate Similarity	NPC471240
0.8049	Intermediate Similarity	NPC476727
0.8049	Intermediate Similarity	NPC472272
0.8049	Intermediate Similarity	NPC476726
0.8049	Intermediate Similarity	NPC155531
0.8049	Intermediate Similarity	NPC215968
0.8026	Intermediate Similarity	NPC3403
0.8025	Intermediate Similarity	NPC475798
0.8025	Intermediate Similarity	NPC127606
0.8025	Intermediate Similarity	NPC86238
0.8	Intermediate Similarity	NPC473238
0.8	Intermediate Similarity	NPC36372
0.8	Intermediate Similarity	NPC472341
0.8	Intermediate Similarity	NPC293609
0.7975	Intermediate Similarity	NPC248944
0.7975	Intermediate Similarity	NPC47149
0.7975	Intermediate Similarity	NPC470609
0.7975	Intermediate Similarity	NPC7479
0.7975	Intermediate Similarity	NPC257296
0.7952	Intermediate Similarity	NPC474657
0.7952	Intermediate Similarity	NPC186145
0.7952	Intermediate Similarity	NPC5943
0.7952	Intermediate Similarity	NPC263802
0.7949	Intermediate Similarity	NPC80089
0.7949	Intermediate Similarity	NPC472499
0.7949	Intermediate Similarity	NPC34046
0.7949	Intermediate Similarity	NPC475
0.7949	Intermediate Similarity	NPC472502
0.7949	Intermediate Similarity	NPC301707
0.7949	Intermediate Similarity	NPC472501
0.7949	Intermediate Similarity	NPC42853
0.7949	Intermediate Similarity	NPC224802
0.7949	Intermediate Similarity	NPC324700
0.7949	Intermediate Similarity	NPC171426
0.7949	Intermediate Similarity	NPC472500
0.7941	Intermediate Similarity	NPC476735
0.7927	Intermediate Similarity	NPC290612
0.7927	Intermediate Similarity	NPC232044
0.7927	Intermediate Similarity	NPC273290
0.7907	Intermediate Similarity	NPC311246
0.7907	Intermediate Similarity	NPC277774
0.7907	Intermediate Similarity	NPC167644
0.7901	Intermediate Similarity	NPC111582
0.7901	Intermediate Similarity	NPC477285
0.7901	Intermediate Similarity	NPC470070
0.7901	Intermediate Similarity	NPC477818
0.7895	Intermediate Similarity	NPC472503
0.7895	Intermediate Similarity	NPC308440
0.7875	Intermediate Similarity	NPC157655
0.7867	Intermediate Similarity	NPC323900

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 NPC304499 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	403
0.1-0.2	4468
0.2-0.3	2997
0.3-0.4	726
0.4-0.5	231
0.5-0.6	175
0.6-0.7	122
0.7-0.8	22
0.8-0.85	4
0.85-0.9	2
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8857	High Similarity	NPD4267	Clinical (unspecified phase)
0.8472	Intermediate Similarity	NPD4787	Phase 1
0.7975	Intermediate Similarity	NPD6928	Phase 2
0.7949	Intermediate Similarity	NPD6115	Approved
0.7949	Intermediate Similarity	NPD6697	Approved
0.7949	Intermediate Similarity	NPD6118	Approved
0.7949	Intermediate Similarity	NPD6114	Approved
0.7821	Intermediate Similarity	NPD6116	Phase 1
0.775	Intermediate Similarity	NPD7525	Registered
0.7692	Intermediate Similarity	NPD6117	Approved
0.7632	Intermediate Similarity	NPD4809	Clinical (unspecified phase)
0.7632	Intermediate Similarity	NPD4808	Clinical (unspecified phase)
0.7564	Intermediate Similarity	NPD3703	Phase 2
0.75	Intermediate Similarity	NPD4244	Approved
0.75	Intermediate Similarity	NPD4245	Approved
0.7436	Intermediate Similarity	NPD6113	Clinical (unspecified phase)
0.7368	Intermediate Similarity	NPD3698	Phase 2
0.7368	Intermediate Similarity	NPD3700	Clinical (unspecified phase)
0.7368	Intermediate Similarity	NPD3699	Clinical (unspecified phase)
0.7303	Intermediate Similarity	NPD8171	Discontinued
0.7237	Intermediate Similarity	NPD5361	Clinical (unspecified phase)
0.7237	Intermediate Similarity	NPD5360	Phase 3
0.7051	Intermediate Similarity	NPD4789	Approved
0.6933	Remote Similarity	NPD371	Approved
0.6905	Remote Similarity	NPD4748	Discontinued
0.6889	Remote Similarity	NPD6700	Approved
0.6889	Remote Similarity	NPD6701	Clinical (unspecified phase)
0.6842	Remote Similarity	NPD3171	Clinical (unspecified phase)
0.6829	Remote Similarity	NPD3701	Clinical (unspecified phase)
0.6813	Remote Similarity	NPD6702	Approved
0.6813	Remote Similarity	NPD6703	Approved
0.6782	Remote Similarity	NPD7338	Clinical (unspecified phase)
0.6774	Remote Similarity	NPD7991	Discontinued
0.675	Remote Similarity	NPD4758	Discontinued
0.6742	Remote Similarity	NPD4751	Clinical (unspecified phase)
0.6707	Remote Similarity	NPD7339	Approved
0.6707	Remote Similarity	NPD3702	Approved
0.6707	Remote Similarity	NPD6942	Approved
0.6706	Remote Similarity	NPD6931	Approved
0.6706	Remote Similarity	NPD6930	Phase 2
0.6705	Remote Similarity	NPD7520	Clinical (unspecified phase)
0.6667	Remote Similarity	NPD6695	Phase 3
0.6667	Remote Similarity	NPD5364	Discontinued
0.6667	Remote Similarity	NPD3671	Phase 1
0.6667	Remote Similarity	NPD4788	Approved
0.6632	Remote Similarity	NPD4755	Approved
0.6588	Remote Similarity	NPD6929	Approved
0.6588	Remote Similarity	NPD7645	Phase 2
0.6582	Remote Similarity	NPD6705	Phase 1
0.6566	Remote Similarity	NPD8170	Clinical (unspecified phase)
0.6559	Remote Similarity	NPD4202	Approved
0.6548	Remote Similarity	NPD6932	Approved
0.6543	Remote Similarity	NPD6081	Approved
0.6543	Remote Similarity	NPD5777	Approved
0.6543	Remote Similarity	NPD4243	Approved
0.6495	Remote Similarity	NPD4696	Approved
0.6495	Remote Similarity	NPD5285	Approved
0.6495	Remote Similarity	NPD4700	Approved
0.6495	Remote Similarity	NPD5286	Approved
0.6452	Remote Similarity	NPD8035	Phase 2
0.6452	Remote Similarity	NPD8034	Phase 2
0.6395	Remote Similarity	NPD6683	Phase 2
0.6392	Remote Similarity	NPD7638	Approved
0.6386	Remote Similarity	NPD6926	Approved
0.6386	Remote Similarity	NPD6924	Approved
0.6386	Remote Similarity	NPD4784	Approved
0.6386	Remote Similarity	NPD4785	Approved
0.6374	Remote Similarity	NPD7750	Discontinued
0.6374	Remote Similarity	NPD7524	Approved
0.6364	Remote Similarity	NPD5211	Phase 2
0.6364	Remote Similarity	NPD5225	Approved
0.6364	Remote Similarity	NPD5224	Approved
0.6364	Remote Similarity	NPD4633	Approved
0.6364	Remote Similarity	NPD5226	Approved
0.6353	Remote Similarity	NPD5776	Phase 2
0.6353	Remote Similarity	NPD6925	Approved
0.6337	Remote Similarity	NPD6675	Approved
0.6337	Remote Similarity	NPD7128	Approved
0.6337	Remote Similarity	NPD5739	Approved
0.6337	Remote Similarity	NPD6402	Approved
0.6333	Remote Similarity	NPD6893	Approved
0.6329	Remote Similarity	NPD4224	Phase 2
0.6327	Remote Similarity	NPD7640	Approved
0.6327	Remote Similarity	NPD7639	Approved
0.6327	Remote Similarity	NPD8418	Phase 2
0.6324	Remote Similarity	NPD384	Approved
0.6324	Remote Similarity	NPD385	Approved
0.6322	Remote Similarity	NPD7514	Phase 3
0.63	Remote Similarity	NPD5174	Approved
0.63	Remote Similarity	NPD5175	Approved
0.6296	Remote Similarity	NPD7328	Approved
0.6296	Remote Similarity	NPD7327	Approved
0.6279	Remote Similarity	NPD7145	Approved
0.6264	Remote Similarity	NPD8308	Discontinued
0.6263	Remote Similarity	NPD5223	Approved
0.625	Remote Similarity	NPD4634	Approved
0.6239	Remote Similarity	NPD7516	Approved
0.6238	Remote Similarity	NPD5141	Approved
0.6237	Remote Similarity	NPD4753	Phase 2
0.6237	Remote Similarity	NPD5328	Approved
0.6235	Remote Similarity	NPD6933	Approved
0.6222	Remote Similarity	NPD4786	Approved
0.6214	Remote Similarity	NPD6881	Approved
0.6214	Remote Similarity	NPD6899	Approved
0.6214	Remote Similarity	NPD7320	Approved
0.62	Remote Similarity	NPD7632	Discontinued
0.619	Remote Similarity	NPD1810	Approved
0.619	Remote Similarity	NPD1811	Approved
0.6176	Remote Similarity	NPD388	Approved
0.6176	Remote Similarity	NPD4767	Approved
0.6176	Remote Similarity	NPD386	Approved
0.6176	Remote Similarity	NPD4768	Approved
0.6154	Remote Similarity	NPD6373	Approved
0.6154	Remote Similarity	NPD6372	Approved
0.6139	Remote Similarity	NPD4754	Approved
0.6136	Remote Similarity	NPD7332	Phase 2
0.6136	Remote Similarity	NPD7509	Discontinued
0.6126	Remote Similarity	NPD8379	Approved
0.6126	Remote Similarity	NPD8378	Approved
0.6126	Remote Similarity	NPD8296	Approved
0.6126	Remote Similarity	NPD8380	Approved
0.6126	Remote Similarity	NPD8335	Approved
0.6122	Remote Similarity	NPD7919	Phase 3
0.6122	Remote Similarity	NPD7920	Phase 3
0.6118	Remote Similarity	NPD4190	Phase 3
0.6118	Remote Similarity	NPD5275	Approved
0.6117	Remote Similarity	NPD5697	Approved
0.6117	Remote Similarity	NPD5701	Approved
0.6105	Remote Similarity	NPD6079	Approved
0.6105	Remote Similarity	NPD7087	Discontinued
0.61	Remote Similarity	NPD1700	Approved
0.61	Remote Similarity	NPD4159	Approved
0.6095	Remote Similarity	NPD7102	Approved
0.6095	Remote Similarity	NPD7290	Approved
0.6095	Remote Similarity	NPD6883	Approved
0.6087	Remote Similarity	NPD3618	Phase 1
0.6067	Remote Similarity	NPD6902	Approved
0.6067	Remote Similarity	NPD6898	Phase 1
0.6061	Remote Similarity	NPD8088	Phase 1
0.6058	Remote Similarity	NPD4730	Approved
0.6058	Remote Similarity	NPD4729	Approved
0.6058	Remote Similarity	NPD5128	Approved
0.6044	Remote Similarity	NPD3665	Phase 1
0.6044	Remote Similarity	NPD3666	Approved
0.6044	Remote Similarity	NPD3133	Approved
0.6038	Remote Similarity	NPD6847	Approved
0.6038	Remote Similarity	NPD6617	Approved
0.6038	Remote Similarity	NPD8130	Phase 1
0.6038	Remote Similarity	NPD6650	Approved
0.6038	Remote Similarity	NPD6649	Approved
0.6038	Remote Similarity	NPD6869	Approved
0.6036	Remote Similarity	NPD8377	Approved
0.6036	Remote Similarity	NPD8294	Approved
0.6024	Remote Similarity	NPD7532	Clinical (unspecified phase)
0.6023	Remote Similarity	NPD4195	Approved
0.6	Remote Similarity	NPD6014	Approved
0.6	Remote Similarity	NPD3667	Approved
0.6	Remote Similarity	NPD6013	Approved
0.6	Remote Similarity	NPD6012	Approved
0.5982	Remote Similarity	NPD8033	Approved
0.5981	Remote Similarity	NPD6882	Approved
0.5981	Remote Similarity	NPD8297	Approved
0.596	Remote Similarity	NPD6083	Phase 2
0.596	Remote Similarity	NPD6084	Phase 2
0.5952	Remote Similarity	NPD7150	Approved
0.5952	Remote Similarity	NPD7152	Approved
0.5952	Remote Similarity	NPD7151	Approved
0.5943	Remote Similarity	NPD5248	Approved
0.5943	Remote Similarity	NPD5250	Approved
0.5943	Remote Similarity	NPD5249	Phase 3
0.5943	Remote Similarity	NPD5251	Approved
0.5943	Remote Similarity	NPD5247	Approved
0.5926	Remote Similarity	NPD4632	Approved
0.5926	Remote Similarity	NPD8133	Approved
0.5918	Remote Similarity	NPD5210	Approved
0.5918	Remote Similarity	NPD4629	Approved
0.5905	Remote Similarity	NPD6011	Approved
0.5904	Remote Similarity	NPD6923	Approved
0.5904	Remote Similarity	NPD6922	Approved
0.5893	Remote Similarity	NPD6059	Approved
0.5893	Remote Similarity	NPD6054	Approved
0.5888	Remote Similarity	NPD5216	Approved
0.5888	Remote Similarity	NPD5217	Approved
0.5888	Remote Similarity	NPD5215	Approved
0.5888	Remote Similarity	NPD6401	Clinical (unspecified phase)
0.5876	Remote Similarity	NPD6399	Phase 3
0.5859	Remote Similarity	NPD5221	Approved
0.5859	Remote Similarity	NPD5220	Clinical (unspecified phase)
0.5859	Remote Similarity	NPD4697	Phase 3
0.5859	Remote Similarity	NPD5222	Approved
0.5833	Remote Similarity	NPD7144	Approved
0.5833	Remote Similarity	NPD2687	Approved
0.5833	Remote Similarity	NPD2686	Approved
0.5833	Remote Similarity	NPD2254	Approved
0.5833	Remote Similarity	NPD7143	Approved
0.5824	Remote Similarity	NPD4221	Approved
0.5824	Remote Similarity	NPD4223	Phase 3
0.581	Remote Similarity	NPD6412	Phase 2
0.5806	Remote Similarity	NPD5329	Approved
0.58	Remote Similarity	NPD5173	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