NPASS Compound

Structure

CID267733 OpenBabel06191716072D 35 38 0 0 1 0 0 0 0 0999 V2000 -3.4263 0.9781 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.6067 2.6765 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.8636 2.0074 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.3988 3.6547 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9125 2.3164 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.4478 3.9637 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7536 3.6036 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0104 2.9344 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 0.0000 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2709 -0.5000 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 -4.7046 3.2946 0.0000 C 0 0 0 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 -2.6831 -1.3090 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.2183 1.9563 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 3.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8660 3.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.0000 3.0000 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 -0.0000 2.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8660 0.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.6831 0.3090 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.7321 -1.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.4641 2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.9921 -2.2601 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.1694 1.6473 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 3.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 4.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 3.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.3253 -1.9135 0.0000 O 0 0 0 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 0.8660 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.4752 1.2872 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2 3 2 0 0 0 0 2 4 1 0 0 0 0 3 5 1 0 0 0 0 4 6 2 0 0 0 0 5 13 2 0 0 0 0 6 13 1 0 0 0 0 7 8 2 0 0 0 0 7 13 1 0 0 0 0 8 16 1 0 0 0 0 9 10 2 0 0 0 0 9 24 1 0 0 0 0 10 32 1 0 0 0 0 11 15 1 0 0 0 0 11 23 1 0 0 0 0 12 25 1 0 0 0 0 14 12 1 1 0 0 0 14 17 1 0 0 0 0 14 33 1 0 0 0 0 15 24 1 6 0 0 0 15 26 1 0 0 0 0 16 27 2 0 0 0 0 16 35 1 0 0 0 0 17 18 1 0 0 0 0 17 28 1 6 0 0 0 18 19 1 0 0 0 0 18 29 1 1 0 0 0 19 21 1 0 0 0 0 19 30 1 6 0 0 0 20 22 1 0 0 0 0 20 23 1 1 0 0 0 20 24 1 0 0 0 0 21 33 1 0 0 0 0 21 34 1 1 0 0 0 22 32 1 0 0 0 0 22 34 1 6 0 0 0 23 1 1 1 0 0 0 23 35 1 0 0 0 0 24 31 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	494.18
Volume:	470.308
LogP:	0.818
LogD:	-0.105
LogS:	-2.896
# Rotatable Bonds:	7
TPSA:	175.37
# H-Bond Aceptor:	11
# H-Bond Donor:	6
# Rings:	4
# Heavy Atoms:	11

MedChem Properties

QED Drug-Likeness Score:	0.207
Synthetic Accessibility Score:	4.864
Fsp3:	0.542
Lipinski Rule-of-5:	Rejected
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:	-6.055
MDCK Permeability:	8.247778896475211e-05
Pgp-inhibitor:	0.001
Pgp-substrate:	0.575
Human Intestinal Absorption (HIA):	0.612
20% Bioavailability (F20%):	0.129
30% Bioavailability (F30%):	0.997

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.116
Plasma Protein Binding (PPB):	62.693206787109375%
Volume Distribution (VD):	0.567
Pgp-substrate:	33.430667877197266%

ADMET: Metabolism

CYP1A2-inhibitor:	0.017
CYP1A2-substrate:	0.13
CYP2C19-inhibitor:	0.014
CYP2C19-substrate:	0.2
CYP2C9-inhibitor:	0.005
CYP2C9-substrate:	0.006
CYP2D6-inhibitor:	0.004
CYP2D6-substrate:	0.043
CYP3A4-inhibitor:	0.146
CYP3A4-substrate:	0.1

ADMET: Excretion

Clearance (CL):	1.714
Half-life (T1/2):	0.688

ADMET: Toxicity

hERG Blockers:	0.021
Human Hepatotoxicity (H-HT):	0.24
Drug-inuced Liver Injury (DILI):	0.296
AMES Toxicity:	0.057
Rat Oral Acute Toxicity:	0.064
Maximum Recommended Daily Dose:	0.05
Skin Sensitization:	0.26
Carcinogencity:	0.872
Eye Corrosion:	0.003
Eye Irritation:	0.024
Respiratory Toxicity:	0.98

Download Data

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

Natural Product: NPC267733

Natural Product ID:	NPC267733
*Common Name:**	Z-Harpagoside
IUPAC Name:	[(1S,4aS,5R,7S,7aS)-4a,5-dihydroxy-7-methyl-1-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-1,5,6,7a-tetrahydrocyclopenta[c]pyran-7-yl] (Z)-3-phenylprop-2-enoate
Synonyms:	Z-harpagoside
Standard InCHIKey:	KVRQGMOSZKPBNS-BCIAEHMOSA-N
Standard InCHI:	InChI=1S/C24H30O11/c1-23(35-16(27)8-7-13-5-3-2-4-6-13)11-15(26)24(31)9-10-32-22(20(23)24)34-21-19(30)18(29)17(28)14(12-25)33-21/h2-10,14-15,17-22,25-26,28-31H,11-12H2,1H3/b8-7-/t14-,15-,17-,18+,19-,20-,21+,22+,23+,24-/m1/s1
SMILES:	C[C@@]1(C[C@H]([C@@]2(C=CO[C@H]([C@H]12)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O)O)O)OC(=O)/C=Cc1ccccc1
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL464888
PubChem CID:	13889700
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0002049] Terpene glycosides [CHEMONTID:0004081] Iridoid O-glycosides

*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
NPO6541	Scrophularia buergeriana	Species	Scrophulariaceae	Eukaryota	roots	n.a.	n.a.	PMID[12444706]
NPO13547	Actinoplanes sp. ATCC 53771	Strain	Micromonosporaceae	Bacteria	n.a.	n.a.	n.a.	PMID[8326323]
NPO13547	Actinoplanes sp. ATCC 53771	Strain	Micromonosporaceae	Bacteria	n.a.	n.a.	n.a.	Database[Article]
NPO6541	Scrophularia buergeriana	Species	Scrophulariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO4802	Scrophularia ningpoensis	Species	Scrophulariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO4802	Scrophularia ningpoensis	Species	Scrophulariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO6541	Scrophularia buergeriana	Species	Scrophulariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO6541	Scrophularia buergeriana	Species	Scrophulariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO4802	Scrophularia ningpoensis	Species	Scrophulariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO4802	Scrophularia ningpoensis	Species	Scrophulariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO6541	Scrophularia buergeriana	Species	Scrophulariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO4802	Scrophularia ningpoensis	Species	Scrophulariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6541	Scrophularia buergeriana	Species	Scrophulariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1976	Sapium pachystachys	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13547	Actinoplanes sp. ATCC 53771	Strain	Micromonosporaceae	Bacteria	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
Others	3

Activity Type	# Activity
Others	3

Target ID	Target Type	Target Name	Activity Type	Activity Relation	Value	Unit	Reference
NPT2	Others	Unspecified	Activity	=	42.5	%	PMID[507639]
NPT2	Others	Unspecified	Activity	=	38.8	%	PMID[507639]
NPT2	Others	Unspecified	Activity	=	26.4	%	PMID[507639]

☑ 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 NPC267733 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	243
0.1-0.2	940
0.2-0.3	2422
0.3-0.4	6244
0.4-0.5	12155
0.5-0.6	16107
0.6-0.7	3941
0.7-0.8	578
0.8-0.85	42
0.85-0.9	17
0.9-0.95	4
0.95-1	4

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC276047
0.9832	High Similarity	NPC145287
0.959	High Similarity	NPC175333
0.9084	High Similarity	NPC49597
0.8992	High Similarity	NPC322503
0.8992	High Similarity	NPC470143
0.8815	High Similarity	NPC302286
0.8815	High Similarity	NPC116104
0.8815	High Similarity	NPC88754
0.8815	High Similarity	NPC237872
0.8815	High Similarity	NPC263397
0.8806	High Similarity	NPC46644
0.8623	High Similarity	NPC37838
0.8613	High Similarity	NPC184464
0.8613	High Similarity	NPC251062
0.8613	High Similarity	NPC478240
0.8529	High Similarity	NPC137501
0.8529	High Similarity	NPC159387
0.8529	High Similarity	NPC154262
0.8529	High Similarity	NPC7518
0.8512	High Similarity	NPC474641
0.85	High Similarity	NPC470825
0.8467	Intermediate Similarity	NPC284957
0.8429	Intermediate Similarity	NPC18789
0.8417	Intermediate Similarity	NPC43584
0.8409	Intermediate Similarity	NPC254819
0.8406	Intermediate Similarity	NPC186296
0.8403	Intermediate Similarity	NPC184633
0.838	Intermediate Similarity	NPC147224
0.8333	Intermediate Similarity	NPC17567
0.831	Intermediate Similarity	NPC478234
0.8268	Intermediate Similarity	NPC229600
0.8252	Intermediate Similarity	NPC240592
0.8252	Intermediate Similarity	NPC117346
0.8239	Intermediate Similarity	NPC308178
0.8207	Intermediate Similarity	NPC229548
0.8207	Intermediate Similarity	NPC89693
0.8207	Intermediate Similarity	NPC478241
0.8195	Intermediate Similarity	NPC319995
0.8195	Intermediate Similarity	NPC289415
0.8194	Intermediate Similarity	NPC269914
0.8194	Intermediate Similarity	NPC478249
0.8182	Intermediate Similarity	NPC478236
0.8182	Intermediate Similarity	NPC96599
0.8138	Intermediate Similarity	NPC194705
0.8134	Intermediate Similarity	NPC475824
0.8116	Intermediate Similarity	NPC31745
0.8116	Intermediate Similarity	NPC220936
0.8085	Intermediate Similarity	NPC202391
0.8085	Intermediate Similarity	NPC296659
0.8069	Intermediate Similarity	NPC289021
0.8069	Intermediate Similarity	NPC158546
0.8041	Intermediate Similarity	NPC475378
0.8027	Intermediate Similarity	NPC478232
0.7971	Intermediate Similarity	NPC27721
0.797	Intermediate Similarity	NPC106677
0.7945	Intermediate Similarity	NPC475379
0.7919	Intermediate Similarity	NPC478248
0.7917	Intermediate Similarity	NPC474564
0.7899	Intermediate Similarity	NPC202729
0.7895	Intermediate Similarity	NPC252114
0.7895	Intermediate Similarity	NPC471157
0.7887	Intermediate Similarity	NPC293154
0.7887	Intermediate Similarity	NPC475213
0.7887	Intermediate Similarity	NPC152796
0.7887	Intermediate Similarity	NPC471139
0.7883	Intermediate Similarity	NPC311492
0.7881	Intermediate Similarity	NPC478265
0.7868	Intermediate Similarity	NPC478255
0.7863	Intermediate Similarity	NPC52097
0.7863	Intermediate Similarity	NPC141970
0.7863	Intermediate Similarity	NPC140561
0.7862	Intermediate Similarity	NPC476092
0.7862	Intermediate Similarity	NPC475218
0.7862	Intermediate Similarity	NPC475447
0.7862	Intermediate Similarity	NPC70236
0.7857	Intermediate Similarity	NPC29607
0.7852	Intermediate Similarity	NPC253595
0.7852	Intermediate Similarity	NPC475484
0.7842	Intermediate Similarity	NPC472132
0.7838	Intermediate Similarity	NPC229354
0.7836	Intermediate Similarity	NPC471882
0.7836	Intermediate Similarity	NPC45224
0.7836	Intermediate Similarity	NPC156692
0.7836	Intermediate Similarity	NPC471881
0.7836	Intermediate Similarity	NPC173150
0.7836	Intermediate Similarity	NPC35288
0.7836	Intermediate Similarity	NPC288416
0.7833	Intermediate Similarity	NPC469527
0.7832	Intermediate Similarity	NPC77922
0.7832	Intermediate Similarity	NPC473281
0.7826	Intermediate Similarity	NPC169398
0.7823	Intermediate Similarity	NPC30563
0.7823	Intermediate Similarity	NPC264784
0.782	Intermediate Similarity	NPC83218
0.782	Intermediate Similarity	NPC126991
0.7793	Intermediate Similarity	NPC473149
0.7786	Intermediate Similarity	NPC473301
0.7786	Intermediate Similarity	NPC475195
0.7786	Intermediate Similarity	NPC11724
0.7786	Intermediate Similarity	NPC475328
0.7778	Intermediate Similarity	NPC225307
0.777	Intermediate Similarity	NPC478235
0.7763	Intermediate Similarity	NPC138993
0.7761	Intermediate Similarity	NPC124878
0.7761	Intermediate Similarity	NPC10883
0.7761	Intermediate Similarity	NPC204214
0.7761	Intermediate Similarity	NPC10121
0.7761	Intermediate Similarity	NPC92283
0.7761	Intermediate Similarity	NPC290276
0.7761	Intermediate Similarity	NPC35338
0.7761	Intermediate Similarity	NPC61181
0.7761	Intermediate Similarity	NPC231888
0.7761	Intermediate Similarity	NPC63404
0.7761	Intermediate Similarity	NPC198918
0.7754	Intermediate Similarity	NPC38420
0.7754	Intermediate Similarity	NPC136608
0.7754	Intermediate Similarity	NPC28836
0.7744	Intermediate Similarity	NPC87153
0.7744	Intermediate Similarity	NPC244454
0.7744	Intermediate Similarity	NPC162925
0.7742	Intermediate Similarity	NPC474148
0.7742	Intermediate Similarity	NPC276061
0.7737	Intermediate Similarity	NPC225384
0.7737	Intermediate Similarity	NPC46137
0.7737	Intermediate Similarity	NPC246869
0.7737	Intermediate Similarity	NPC233692
0.7737	Intermediate Similarity	NPC138777
0.7737	Intermediate Similarity	NPC235294
0.7737	Intermediate Similarity	NPC239358
0.7724	Intermediate Similarity	NPC475539
0.7724	Intermediate Similarity	NPC143246
0.7724	Intermediate Similarity	NPC474268
0.7724	Intermediate Similarity	NPC474234
0.7724	Intermediate Similarity	NPC119773
0.7721	Intermediate Similarity	NPC295970
0.771	Intermediate Similarity	NPC476872
0.7708	Intermediate Similarity	NPC63304
0.7704	Intermediate Similarity	NPC58061
0.7704	Intermediate Similarity	NPC103533
0.7704	Intermediate Similarity	NPC230331
0.7687	Intermediate Similarity	NPC77651
0.7687	Intermediate Similarity	NPC28069
0.7681	Intermediate Similarity	NPC472248
0.7669	Intermediate Similarity	NPC470815
0.7662	Intermediate Similarity	NPC476011
0.7662	Intermediate Similarity	NPC206815
0.766	Intermediate Similarity	NPC469364
0.766	Intermediate Similarity	NPC65262
0.766	Intermediate Similarity	NPC101686
0.7655	Intermediate Similarity	NPC475528
0.7651	Intermediate Similarity	NPC469456
0.7647	Intermediate Similarity	NPC474936
0.7647	Intermediate Similarity	NPC146540
0.7647	Intermediate Similarity	NPC471024
0.7632	Intermediate Similarity	NPC329997
0.763	Intermediate Similarity	NPC114096
0.7628	Intermediate Similarity	NPC130730
0.7628	Intermediate Similarity	NPC301910
0.7626	Intermediate Similarity	NPC254398
0.7623	Intermediate Similarity	NPC47286
0.7619	Intermediate Similarity	NPC189631
0.7609	Intermediate Similarity	NPC233860
0.7609	Intermediate Similarity	NPC281798
0.76	Intermediate Similarity	NPC469699
0.7582	Intermediate Similarity	NPC179914
0.7574	Intermediate Similarity	NPC231627
0.7574	Intermediate Similarity	NPC471025
0.7574	Intermediate Similarity	NPC148026
0.7571	Intermediate Similarity	NPC200154
0.7568	Intermediate Similarity	NPC478123
0.7568	Intermediate Similarity	NPC62792
0.7568	Intermediate Similarity	NPC298072
0.7566	Intermediate Similarity	NPC478266
0.7561	Intermediate Similarity	NPC37714
0.7561	Intermediate Similarity	NPC152384
0.7554	Intermediate Similarity	NPC473924
0.7554	Intermediate Similarity	NPC473285
0.7552	Intermediate Similarity	NPC325078
0.7538	Intermediate Similarity	NPC219656
0.7536	Intermediate Similarity	NPC305162
0.7518	Intermediate Similarity	NPC93632
0.7518	Intermediate Similarity	NPC237182
0.7518	Intermediate Similarity	NPC476870
0.7518	Intermediate Similarity	NPC263829
0.7518	Intermediate Similarity	NPC226101
0.7518	Intermediate Similarity	NPC301857
0.7517	Intermediate Similarity	NPC35097
0.7517	Intermediate Similarity	NPC69367
0.75	Intermediate Similarity	NPC476442
0.75	Intermediate Similarity	NPC476173
0.75	Intermediate Similarity	NPC28637
0.75	Intermediate Similarity	NPC147032
0.75	Intermediate Similarity	NPC136962
0.75	Intermediate Similarity	NPC109990
0.75	Intermediate Similarity	NPC215512
0.7483	Intermediate Similarity	NPC473147
0.7483	Intermediate Similarity	NPC321184
0.7483	Intermediate Similarity	NPC321638
0.7483	Intermediate Similarity	NPC328273

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 NPC267733 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	199
0.1-0.2	641
0.2-0.3	1537
0.3-0.4	3428
0.4-0.5	2311
0.5-0.6	924
0.6-0.7	103
0.7-0.8	7
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
0.7429	Intermediate Similarity	NPD7966	Clinical (unspecified phase)
0.7391	Intermediate Similarity	NPD7685	Pre-registration
0.7372	Intermediate Similarity	NPD6007	Clinical (unspecified phase)
0.7361	Intermediate Similarity	NPD7266	Discontinued
0.7344	Intermediate Similarity	NPD969	Suspended
0.7258	Intermediate Similarity	NPD5738	Clinical (unspecified phase)
0.7222	Intermediate Similarity	NPD6685	Approved
0.7164	Intermediate Similarity	NPD7503	Approved
0.7111	Intermediate Similarity	NPD5125	Phase 3
0.7111	Intermediate Similarity	NPD5126	Approved
0.7007	Intermediate Similarity	NPD1091	Approved
0.6984	Remote Similarity	NPD6647	Phase 2
0.6984	Remote Similarity	NPD5765	Approved
0.6947	Remote Similarity	NPD6912	Phase 3
0.6883	Remote Similarity	NPD1653	Approved
0.6849	Remote Similarity	NPD6653	Approved
0.6838	Remote Similarity	NPD7741	Discontinued
0.6833	Remote Similarity	NPD689	Discontinued
0.6829	Remote Similarity	NPD7799	Discontinued
0.6815	Remote Similarity	NPD694	Clinical (unspecified phase)
0.6807	Remote Similarity	NPD1282	Approved
0.6797	Remote Similarity	NPD5909	Discontinued
0.6688	Remote Similarity	NPD8389	Clinical (unspecified phase)
0.6667	Remote Similarity	NPD6006	Clinical (unspecified phase)
0.6667	Remote Similarity	NPD6002	Phase 3
0.6667	Remote Similarity	NPD2067	Discontinued
0.6667	Remote Similarity	NPD5763	Approved
0.6667	Remote Similarity	NPD5762	Approved
0.6667	Remote Similarity	NPD6003	Clinical (unspecified phase)
0.6667	Remote Similarity	NPD6005	Phase 3
0.6667	Remote Similarity	NPD6004	Phase 3
0.6601	Remote Similarity	NPD7274	Clinical (unspecified phase)
0.6573	Remote Similarity	NPD6362	Approved
0.6554	Remote Similarity	NPD5123	Clinical (unspecified phase)
0.6554	Remote Similarity	NPD5124	Phase 1
0.6547	Remote Similarity	NPD8033	Approved
0.6544	Remote Similarity	NPD690	Clinical (unspecified phase)
0.6528	Remote Similarity	NPD5647	Approved
0.6515	Remote Similarity	NPD6406	Approved
0.6507	Remote Similarity	NPD5952	Clinical (unspecified phase)
0.6496	Remote Similarity	NPD4198	Discontinued
0.6494	Remote Similarity	NPD6190	Approved
0.6489	Remote Similarity	NPD5048	Discontinued
0.6471	Remote Similarity	NPD1652	Phase 2
0.6467	Remote Similarity	NPD4978	Clinical (unspecified phase)
0.6458	Remote Similarity	NPD3094	Phase 2
0.6452	Remote Similarity	NPD7236	Approved
0.6449	Remote Similarity	NPD7328	Approved
0.6449	Remote Similarity	NPD7327	Approved
0.6442	Remote Similarity	NPD4381	Clinical (unspecified phase)
0.6424	Remote Similarity	NPD7033	Discontinued
0.6406	Remote Similarity	NPD8029	Clinical (unspecified phase)
0.6403	Remote Similarity	NPD7516	Approved
0.6358	Remote Similarity	NPD8455	Phase 2
0.6358	Remote Similarity	NPD7097	Phase 1
0.6357	Remote Similarity	NPD8377	Approved
0.6357	Remote Similarity	NPD8294	Approved
0.6352	Remote Similarity	NPD7239	Suspended
0.6325	Remote Similarity	NPD7199	Phase 2
0.6323	Remote Similarity	NPD4628	Phase 3
0.6322	Remote Similarity	NPD8055	Clinical (unspecified phase)
0.6312	Remote Similarity	NPD8380	Approved
0.6312	Remote Similarity	NPD8378	Approved
0.6312	Remote Similarity	NPD8379	Approved
0.6312	Remote Similarity	NPD8335	Approved
0.6312	Remote Similarity	NPD8296	Approved
0.6304	Remote Similarity	NPD2629	Approved
0.6296	Remote Similarity	NPD37	Approved
0.6294	Remote Similarity	NPD8470	Clinical (unspecified phase)
0.628	Remote Similarity	NPD4965	Approved
0.628	Remote Similarity	NPD4966	Approved
0.628	Remote Similarity	NPD4967	Phase 2
0.6269	Remote Similarity	NPD1358	Approved
0.6269	Remote Similarity	NPD6686	Approved
0.6267	Remote Similarity	NPD4140	Approved
0.6242	Remote Similarity	NPD5058	Phase 3
0.6235	Remote Similarity	NPD7228	Approved
0.6225	Remote Similarity	NPD4340	Discontinued
0.6207	Remote Similarity	NPD8312	Approved
0.6207	Remote Similarity	NPD8313	Approved
0.6205	Remote Similarity	NPD6234	Discontinued
0.6203	Remote Similarity	NPD6143	Clinical (unspecified phase)
0.6194	Remote Similarity	NPD3134	Approved
0.619	Remote Similarity	NPD6085	Phase 2
0.619	Remote Similarity	NPD5740	Clinical (unspecified phase)
0.6188	Remote Similarity	NPD5403	Approved
0.6185	Remote Similarity	NPD6559	Discontinued
0.6181	Remote Similarity	NPD3092	Approved
0.6169	Remote Similarity	NPD7137	Phase 2
0.6159	Remote Similarity	NPD7094	Approved
0.6159	Remote Similarity	NPD6858	Approved
0.6154	Remote Similarity	NPD6674	Discontinued
0.6154	Remote Similarity	NPD7184	Clinical (unspecified phase)
0.6149	Remote Similarity	NPD2861	Phase 2
0.6149	Remote Similarity	NPD5736	Approved
0.614	Remote Similarity	NPD3818	Discontinued
0.6138	Remote Similarity	NPD7507	Approved
0.6131	Remote Similarity	NPD8127	Discontinued
0.6131	Remote Similarity	NPD2181	Clinical (unspecified phase)
0.6127	Remote Similarity	NPD9545	Approved
0.6122	Remote Similarity	NPD2797	Approved
0.6118	Remote Similarity	NPD5735	Approved
0.6118	Remote Similarity	NPD6355	Discontinued
0.6115	Remote Similarity	NPD2575	Approved
0.6115	Remote Similarity	NPD6010	Discontinued
0.6115	Remote Similarity	NPD1878	Clinical (unspecified phase)
0.6111	Remote Similarity	NPD7457	Clinical (unspecified phase)
0.6105	Remote Similarity	NPD7054	Approved
0.6105	Remote Similarity	NPD7804	Clinical (unspecified phase)
0.6103	Remote Similarity	NPD2182	Approved
0.6094	Remote Similarity	NPD5122	Clinical (unspecified phase)
0.6093	Remote Similarity	NPD6233	Phase 2
0.6084	Remote Similarity	NPD7058	Phase 2
0.6084	Remote Similarity	NPD7057	Phase 3
0.6084	Remote Similarity	NPD8513	Phase 3
0.6074	Remote Similarity	NPD7028	Phase 2
0.6074	Remote Similarity	NPD4380	Phase 2
0.6069	Remote Similarity	NPD3705	Approved
0.6069	Remote Similarity	NPD7472	Approved
0.6069	Remote Similarity	NPD422	Phase 1
0.6062	Remote Similarity	NPD5401	Approved
0.6062	Remote Similarity	NPD7004	Clinical (unspecified phase)
0.6057	Remote Similarity	NPD4338	Clinical (unspecified phase)
0.6056	Remote Similarity	NPD7879	Clinical (unspecified phase)
0.6054	Remote Similarity	NPD3225	Approved
0.6042	Remote Similarity	NPD5306	Approved
0.6042	Remote Similarity	NPD5305	Approved
0.6034	Remote Similarity	NPD6797	Phase 2
0.6031	Remote Similarity	NPD5926	Approved
0.6031	Remote Similarity	NPD9495	Approved
0.6029	Remote Similarity	NPD290	Approved
0.6027	Remote Similarity	NPD6637	Approved
0.6026	Remote Similarity	NPD3268	Approved
0.6026	Remote Similarity	NPD3764	Approved
0.6025	Remote Similarity	NPD6273	Approved
0.6024	Remote Similarity	NPD5402	Approved
0.6014	Remote Similarity	NPD4141	Clinical (unspecified phase)
0.6014	Remote Similarity	NPD7319	Approved
0.6013	Remote Similarity	NPD7488	Clinical (unspecified phase)
0.6013	Remote Similarity	NPD6398	Clinical (unspecified phase)
0.6	Remote Similarity	NPD7240	Approved
0.6	Remote Similarity	NPD2613	Approved
0.6	Remote Similarity	NPD6801	Discontinued
0.6	Remote Similarity	NPD7251	Discontinued
0.6	Remote Similarity	NPD3496	Discontinued
0.5987	Remote Similarity	NPD6663	Approved
0.5987	Remote Similarity	NPD2424	Discontinued
0.5985	Remote Similarity	NPD7798	Approved
0.5985	Remote Similarity	NPD2066	Phase 3
0.5984	Remote Similarity	NPD7838	Discovery
0.5977	Remote Similarity	NPD7074	Phase 3
0.5972	Remote Similarity	NPD8516	Approved
0.5972	Remote Similarity	NPD8517	Approved
0.5972	Remote Similarity	NPD8515	Approved
0.5972	Remote Similarity	NPD1357	Approved
0.5971	Remote Similarity	NPD6053	Discontinued
0.5966	Remote Similarity	NPD7808	Phase 3
0.596	Remote Similarity	NPD3027	Phase 3
0.5959	Remote Similarity	NPD4807	Approved
0.5959	Remote Similarity	NPD4806	Approved
0.5952	Remote Similarity	NPD7075	Discontinued
0.5948	Remote Similarity	NPD3620	Phase 2
0.5948	Remote Similarity	NPD3619	Clinical (unspecified phase)
0.5948	Remote Similarity	NPD4060	Phase 1
0.5935	Remote Similarity	NPD3971	Phase 1
0.5933	Remote Similarity	NPD3664	Approved
0.5933	Remote Similarity	NPD3663	Approved
0.5933	Remote Similarity	NPD3662	Phase 3
0.5933	Remote Similarity	NPD3661	Approved
0.5929	Remote Similarity	NPD7843	Approved
0.5926	Remote Similarity	NPD7314	Clinical (unspecified phase)
0.5921	Remote Similarity	NPD6798	Discontinued
0.592	Remote Similarity	NPD4249	Approved
0.5915	Remote Similarity	NPD7157	Approved
0.5915	Remote Similarity	NPD7458	Discontinued
0.5912	Remote Similarity	NPD7982	Clinical (unspecified phase)
0.5909	Remote Similarity	NPD8368	Discontinued
0.5909	Remote Similarity	NPD230	Phase 1
0.5909	Remote Similarity	NPD1933	Approved
0.5906	Remote Similarity	NPD2626	Approved
0.5906	Remote Similarity	NPD2627	Approved
0.5906	Remote Similarity	NPD2159	Approved
0.5906	Remote Similarity	NPD2625	Approved
0.5906	Remote Similarity	NPD2160	Approved
0.5906	Remote Similarity	NPD2628	Approved
0.5903	Remote Similarity	NPD4479	Discontinued
0.5903	Remote Similarity	NPD3091	Approved
0.5899	Remote Similarity	NPD8413	Clinical (unspecified phase)
0.5899	Remote Similarity	NPD8407	Phase 2
0.5894	Remote Similarity	NPD4908	Phase 1
0.5894	Remote Similarity	NPD4617	Approved
0.5894	Remote Similarity	NPD5203	Approved
0.5894	Remote Similarity	NPD4620	Approved
0.5894	Remote Similarity	NPD5201	Approved
0.5893	Remote Similarity	NPD4868	Clinical (unspecified phase)
0.589	Remote Similarity	NPD4135	Approved
0.589	Remote Similarity	NPD6980	Clinical (unspecified phase)
0.589	Remote Similarity	NPD4106	Approved
0.589	Remote Similarity	NPD4136	Approved
0.5887	Remote Similarity	NPD2652	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