NPASS Compound

Structure

CID3906 OpenBabel06191715322D 29 32 0 0 1 0 0 0 0 0999 V2000 2.2130 -1.1293 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3660 -4.0388 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6001 3.7973 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0007 1.5527 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7572 -0.7826 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5000 2.1906 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4010 1.7568 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1340 2.4369 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3090 -1.9511 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8932 -0.3963 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4010 1.7568 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -1.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.6235 0.7818 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.5000 -2.5388 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0896 2.1422 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6235 0.7818 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0000 -1.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.0000 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3090 -1.9511 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3121 1.1672 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5791 0.4871 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5984 0.5593 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 3.8681 -0.6188 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.2601 -2.2601 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.5000 -3.5388 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.8226 2.8223 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.2677 0.8725 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.8016 -0.4879 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 10 1 0 0 0 0 2 26 1 0 0 0 0 3 27 1 0 0 0 0 4 28 1 0 0 0 0 5 29 1 0 0 0 0 6 7 1 0 0 0 0 6 11 1 0 0 0 0 7 13 1 0 0 0 0 8 11 2 0 0 0 0 8 15 1 0 0 0 0 9 14 2 0 0 0 0 10 23 2 3 0 0 0 10 24 1 0 0 0 0 11 16 1 0 0 0 0 12 9 1 6 0 0 0 12 17 1 0 0 0 0 12 18 1 0 0 0 0 13 19 1 0 0 0 0 13 23 1 6 0 0 0 14 20 1 0 0 0 0 14 26 1 0 0 0 0 15 21 2 0 0 0 0 15 27 1 0 0 0 0 16 17 1 0 0 0 0 16 22 2 0 0 0 0 17 19 2 0 0 0 0 18 19 1 6 0 0 0 18 20 1 0 0 0 0 20 25 2 0 0 0 0 21 22 1 0 0 0 0 21 28 1 0 0 0 0 22 29 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	399.17
Volume:	400.125
LogP:	2.102
LogD:	0.926
LogS:	-2.608
# Rotatable Bonds:	5
TPSA:	86.58
# H-Bond Aceptor:	7
# H-Bond Donor:	1
# Rings:	4
# Heavy Atoms:	7

MedChem Properties

QED Drug-Likeness Score:	0.83
Synthetic Accessibility Score:	4.524
Fsp3:	0.455
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	1
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.69
MDCK Permeability:	3.093889245064929e-05
Pgp-inhibitor:	0.007
Pgp-substrate:	0.009
Human Intestinal Absorption (HIA):	0.02
20% Bioavailability (F20%):	0.004
30% Bioavailability (F30%):	0.046

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.552
Plasma Protein Binding (PPB):	90.76921844482422%
Volume Distribution (VD):	1.229
Pgp-substrate:	6.969488620758057%

ADMET: Metabolism

CYP1A2-inhibitor:	0.058
CYP1A2-substrate:	0.979
CYP2C19-inhibitor:	0.024
CYP2C19-substrate:	0.933
CYP2C9-inhibitor:	0.025
CYP2C9-substrate:	0.442
CYP2D6-inhibitor:	0.019
CYP2D6-substrate:	0.602
CYP3A4-inhibitor:	0.099
CYP3A4-substrate:	0.923

ADMET: Excretion

Clearance (CL):	4.74
Half-life (T1/2):	0.131

ADMET: Toxicity

hERG Blockers:	0.226
Human Hepatotoxicity (H-HT):	0.529
Drug-inuced Liver Injury (DILI):	0.673
AMES Toxicity:	0.085
Rat Oral Acute Toxicity:	0.58
Maximum Recommended Daily Dose:	0.811
Skin Sensitization:	0.193
Carcinogencity:	0.03
Eye Corrosion:	0.003
Eye Irritation:	0.013
Respiratory Toxicity:	0.836

Download Data

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

Natural Product: NPC3906

Natural Product ID:	NPC3906
*Common Name:**	VKPVZFOUXUQJMW-FHSNZYRGSA-N
IUPAC Name:	n.a.
Synonyms:	Beta-Lumicolchicine
Standard InCHIKey:	VKPVZFOUXUQJMW-FHSNZYRGSA-N
Standard InCHI:	InChI=1S/C22H25NO6/c1-10(24)23-13-7-6-11-8-15(27-3)21(28-4)22(29-5)16(11)17-12-9-14(26-2)20(25)18(12)19(13)17/h8-9,12-13,18H,6-7H2,1-5H3,(H,23,24)/t12-,13+,18-/m1/s1
SMILES:	COC1=C[C@H]2[C@@H](C1=O)C1=C2c2c(CC[C@@H]1N=C(O)C)cc(c(c2OC)OC)OC
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL527025
PubChem CID:	244898
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000279] Alkaloids and derivatives [CHEMONTID:0003777] Lumicolchicine 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
NPO24146	Colchicum brachyphyllum	Species	Colchicaceae	Eukaryota	n.a.	Jordanian	n.a.	PMID[15730238]
NPO22241	Alangium villosum	Species	Cornaceae	Eukaryota	stem bark	Ceram, Indonesia	1998	PMID[18327911]
NPO22241	Alangium villosum	Species	Cornaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[32372642]
NPO4250	Gloriosa superba	Species	Colchicaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[32372642]
NPO26551	Artemisia ludoviciana	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO4250	Gloriosa superba	Species	Colchicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO1559	Pinus palustris	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO1559	Pinus palustris	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO4250	Gloriosa superba	Species	Colchicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO6856.1	Artemisia ludoviciana subsp. mexicana	Subspecies	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO26551	Artemisia ludoviciana	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO7149	Dalbergia melanoxylon	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO26551	Artemisia ludoviciana	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO7149	Dalbergia melanoxylon	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO7149	Dalbergia melanoxylon	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24146	Colchicum brachyphyllum	Species	Colchicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22241	Alangium villosum	Species	Cornaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26551	Artemisia ludoviciana	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1559	Pinus palustris	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6856.1	Artemisia ludoviciana subsp. mexicana	Subspecies	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4250	Gloriosa superba	Species	Colchicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]

☑ Note for Reference:
In addition to directly collecting NP source organism data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated them from below databases:
☉ UNPD: Universal Natural Products Database [PMID: 23638153].
☉ StreptomeDB: a database of streptomycetes natural products [PMID: 33051671].
☉ TM-MC: a database of medicinal materials and chemical compounds in Northeast Asian traditional medicine [PMID: 26156871].
☉ TCM@Taiwan: a Traditional Chinese Medicine database [PMID: 21253603].
☉ TCMID: a Traditional Chinese Medicine database [PMID: 29106634].
☉ TCMSP: The traditional Chinese medicine systems pharmacology database and analysis platform [PMID: 24735618].
☉ HerDing: a herb recommendation system to treat diseases using genes and chemicals [PMID: 26980517].
☉ MetaboLights: a metabolomics database [PMID: 27010336].
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

NP Quantity Composition/Concentration

Organism ID	NP ID	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference

☑ Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP quantitative records for specific NP domains (e.g., NPS from foods or herbs) from domain-specific databases. These databases include:
☉ DUKE: Dr. Duke's Phytochemical and Ethnobotanical Databases.
☉ PHENOL EXPLORER: is the first comprehensive database on polyphenol content in foods [PMID: 24103452], its homepage can be accessed at here.
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

Biological Activity

Activity Type	# Activity
EC50	3
IC50	2
MIC	4
Others	1
Potency	3

Activity Type	# Activity
Cell Line	3
Individual Protein	2
Organism	7
Others	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT83	Cell Line	MCF7	Homo sapiens	EC50	=	1500.0	nM	PMID[450816]
NPT397	Cell Line	NCI-H460	Homo sapiens	EC50	=	2100.0	nM	PMID[450816]
NPT395	Cell Line	SF-268	Homo sapiens	EC50	=	3200.0	nM	PMID[450816]
NPT135	Individual Protein	Chromobox protein homolog 1	Homo sapiens	Potency	n.a.	79432.8	nM	PMID[450817]
NPT10	Individual Protein	Geminin	Homo sapiens	Potency	n.a.	326.4	nM	PMID[450817]
NPT140	Organism	Artemia	Artemia	LC50	=	74.6	ug.mL-1	PMID[450816]
NPT729	Organism	Micrococcus luteus	Micrococcus luteus	MIC	>	500.0	ug.mL-1	PMID[450816]
NPT602	Organism	Mycobacterium smegmatis	Mycobacterium smegmatis	MIC	>	500.0	ug.mL-1	PMID[450816]
NPT312	Organism	Saccharomyces cerevisiae	Saccharomyces cerevisiae	MIC	>	500.0	ug.mL-1	PMID[450816]
NPT21	Organism	Aspergillus niger	Aspergillus niger	MIC	>	500.0	ug.mL-1	PMID[450816]
NPT2	Others	Unspecified		Potency	=	92.0	nM	PMID[450817]
NPT20555	ORGANISM	SARS-CoV-2	Severe acute respiratory syndrome coronavirus 2	IC50	>	20000.0	nM	PMID[450819]
NPT20555	ORGANISM	SARS-CoV-2	Severe acute respiratory syndrome coronavirus 2	IC50	>	19952.62	nM	PMID[450819]

☑ 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 NPC3906 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	260
0.1-0.2	1275
0.2-0.3	4579
0.3-0.4	12651
0.4-0.5	5467
0.5-0.6	8569
0.6-0.7	9616
0.7-0.8	270
0.8-0.85	2
0.85-0.9	7
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
0.9161	High Similarity	NPC226941
0.9161	High Similarity	NPC14005
0.9161	High Similarity	NPC108957
0.8917	High Similarity	NPC44642
0.8882	High Similarity	NPC189782
0.8875	High Similarity	NPC202839
0.8875	High Similarity	NPC66678
0.8553	High Similarity	NPC218575
0.8344	Intermediate Similarity	NPC190931
0.8214	Intermediate Similarity	NPC188120
0.8214	Intermediate Similarity	NPC286790
0.8214	Intermediate Similarity	NPC53146
0.7811	Intermediate Similarity	NPC329837
0.7665	Intermediate Similarity	NPC177830
0.7605	Intermediate Similarity	NPC478189
0.753	Intermediate Similarity	NPC474446
0.75	Intermediate Similarity	NPC470642
0.747	Intermediate Similarity	NPC232883
0.7455	Intermediate Similarity	NPC474966
0.7425	Intermediate Similarity	NPC476362
0.7423	Intermediate Similarity	NPC470962
0.7412	Intermediate Similarity	NPC58661
0.741	Intermediate Similarity	NPC16353
0.7407	Intermediate Similarity	NPC471182
0.7391	Intermediate Similarity	NPC474009
0.7386	Intermediate Similarity	NPC68328
0.7368	Intermediate Similarity	NPC272566
0.7368	Intermediate Similarity	NPC474414
0.7366	Intermediate Similarity	NPC63152
0.7365	Intermediate Similarity	NPC474982
0.7337	Intermediate Similarity	NPC18306
0.7337	Intermediate Similarity	NPC77598
0.7337	Intermediate Similarity	NPC304821
0.7326	Intermediate Similarity	NPC169742
0.7317	Intermediate Similarity	NPC46947
0.7314	Intermediate Similarity	NPC477410
0.7302	Intermediate Similarity	NPC281629
0.7284	Intermediate Similarity	NPC145769
0.7278	Intermediate Similarity	NPC291847
0.7278	Intermediate Similarity	NPC30720
0.7273	Intermediate Similarity	NPC196231
0.7273	Intermediate Similarity	NPC144284
0.7273	Intermediate Similarity	NPC476569
0.7268	Intermediate Similarity	NPC298339
0.7267	Intermediate Similarity	NPC239302
0.7267	Intermediate Similarity	NPC220577
0.7262	Intermediate Similarity	NPC207732
0.7261	Intermediate Similarity	NPC173608
0.7257	Intermediate Similarity	NPC475780
0.7256	Intermediate Similarity	NPC296898
0.7251	Intermediate Similarity	NPC8337
0.7251	Intermediate Similarity	NPC85747
0.7247	Intermediate Similarity	NPC284842
0.7243	Intermediate Similarity	NPC214629
0.7241	Intermediate Similarity	NPC234485
0.7235	Intermediate Similarity	NPC474999
0.7235	Intermediate Similarity	NPC117463
0.7232	Intermediate Similarity	NPC255607
0.7232	Intermediate Similarity	NPC3375
0.7229	Intermediate Similarity	NPC19158
0.7225	Intermediate Similarity	NPC474993
0.7222	Intermediate Similarity	NPC231371
0.7219	Intermediate Similarity	NPC474799
0.7219	Intermediate Similarity	NPC472560
0.7219	Intermediate Similarity	NPC157133
0.7216	Intermediate Similarity	NPC104876
0.7216	Intermediate Similarity	NPC245891
0.7212	Intermediate Similarity	NPC44573
0.7207	Intermediate Similarity	NPC473748
0.7202	Intermediate Similarity	NPC18211
0.7202	Intermediate Similarity	NPC119663
0.72	Intermediate Similarity	NPC469474
0.7193	Intermediate Similarity	NPC476058
0.7188	Intermediate Similarity	NPC471031
0.7188	Intermediate Similarity	NPC469689
0.7188	Intermediate Similarity	NPC150809
0.7186	Intermediate Similarity	NPC46180
0.7186	Intermediate Similarity	NPC110419
0.7184	Intermediate Similarity	NPC473664
0.7184	Intermediate Similarity	NPC127172
0.7179	Intermediate Similarity	NPC475768
0.7176	Intermediate Similarity	NPC153644
0.7169	Intermediate Similarity	NPC322021
0.7168	Intermediate Similarity	NPC28724
0.7168	Intermediate Similarity	NPC78505
0.7166	Intermediate Similarity	NPC208890
0.716	Intermediate Similarity	NPC476841
0.716	Intermediate Similarity	NPC476843
0.716	Intermediate Similarity	NPC473934
0.7159	Intermediate Similarity	NPC226428
0.7159	Intermediate Similarity	NPC26353
0.7159	Intermediate Similarity	NPC476340
0.7151	Intermediate Similarity	NPC474560
0.7151	Intermediate Similarity	NPC475170
0.7151	Intermediate Similarity	NPC476822
0.7151	Intermediate Similarity	NPC127402
0.7151	Intermediate Similarity	NPC476579
0.7143	Intermediate Similarity	NPC312256
0.7143	Intermediate Similarity	NPC28326
0.7143	Intermediate Similarity	NPC172673
0.7143	Intermediate Similarity	NPC185607
0.7143	Intermediate Similarity	NPC79998
0.7135	Intermediate Similarity	NPC470511
0.7135	Intermediate Similarity	NPC294972
0.7135	Intermediate Similarity	NPC201560
0.7135	Intermediate Similarity	NPC180306
0.7135	Intermediate Similarity	NPC24465
0.7135	Intermediate Similarity	NPC299923
0.7134	Intermediate Similarity	NPC208760
0.7134	Intermediate Similarity	NPC72796
0.7134	Intermediate Similarity	NPC211386
0.7134	Intermediate Similarity	NPC44245
0.7127	Intermediate Similarity	NPC477115
0.7126	Intermediate Similarity	NPC28103
0.7126	Intermediate Similarity	NPC304954
0.7118	Intermediate Similarity	NPC87295
0.7117	Intermediate Similarity	NPC32778
0.7112	Intermediate Similarity	NPC474661
0.7112	Intermediate Similarity	NPC475919
0.7111	Intermediate Similarity	NPC83198
0.7111	Intermediate Similarity	NPC204908
0.7111	Intermediate Similarity	NPC475953
0.7111	Intermediate Similarity	NPC182257
0.711	Intermediate Similarity	NPC472279
0.711	Intermediate Similarity	NPC85131
0.711	Intermediate Similarity	NPC62354
0.711	Intermediate Similarity	NPC103509
0.7104	Intermediate Similarity	NPC35680
0.7102	Intermediate Similarity	NPC477380
0.7101	Intermediate Similarity	NPC143092
0.7101	Intermediate Similarity	NPC3732
0.7101	Intermediate Similarity	NPC476054
0.7095	Intermediate Similarity	NPC48860
0.7095	Intermediate Similarity	NPC13916
0.7095	Intermediate Similarity	NPC469512
0.7095	Intermediate Similarity	NPC474858
0.7095	Intermediate Similarity	NPC264850
0.7093	Intermediate Similarity	NPC261548
0.7093	Intermediate Similarity	NPC474903
0.7093	Intermediate Similarity	NPC237904
0.7093	Intermediate Similarity	NPC276665
0.7093	Intermediate Similarity	NPC265473
0.7089	Intermediate Similarity	NPC105513
0.7088	Intermediate Similarity	NPC247136
0.7086	Intermediate Similarity	NPC178195
0.7086	Intermediate Similarity	NPC348849
0.7083	Intermediate Similarity	NPC472332
0.7083	Intermediate Similarity	NPC472335
0.7081	Intermediate Similarity	NPC153547
0.7081	Intermediate Similarity	NPC115906
0.7079	Intermediate Similarity	NPC59567
0.7079	Intermediate Similarity	NPC301089
0.7076	Intermediate Similarity	NPC165389
0.7076	Intermediate Similarity	NPC12377
0.7076	Intermediate Similarity	NPC310259
0.7076	Intermediate Similarity	NPC137352
0.7076	Intermediate Similarity	NPC295297
0.7076	Intermediate Similarity	NPC183083
0.7072	Intermediate Similarity	NPC477517
0.7069	Intermediate Similarity	NPC76376
0.7069	Intermediate Similarity	NPC228662
0.7069	Intermediate Similarity	NPC265862
0.7069	Intermediate Similarity	NPC92747
0.7069	Intermediate Similarity	NPC151425
0.7069	Intermediate Similarity	NPC236769
0.7069	Intermediate Similarity	NPC475557
0.7069	Intermediate Similarity	NPC476335
0.7062	Intermediate Similarity	NPC477885
0.7062	Intermediate Similarity	NPC37543
0.7062	Intermediate Similarity	NPC199463
0.7062	Intermediate Similarity	NPC474990
0.7062	Intermediate Similarity	NPC472963
0.7059	Intermediate Similarity	NPC27106
0.7059	Intermediate Similarity	NPC105213
0.7056	Intermediate Similarity	NPC475865
0.7056	Intermediate Similarity	NPC469518
0.7056	Intermediate Similarity	NPC469475
0.7055	Intermediate Similarity	NPC280476
0.7055	Intermediate Similarity	NPC119985
0.7055	Intermediate Similarity	NPC102256
0.7055	Intermediate Similarity	NPC475856
0.7049	Intermediate Similarity	NPC207721
0.7045	Intermediate Similarity	NPC80534
0.7045	Intermediate Similarity	NPC56786
0.7045	Intermediate Similarity	NPC38898
0.7045	Intermediate Similarity	NPC476363
0.7045	Intermediate Similarity	NPC31018
0.7045	Intermediate Similarity	NPC195766
0.7045	Intermediate Similarity	NPC117154
0.7045	Intermediate Similarity	NPC255807
0.7045	Intermediate Similarity	NPC206736
0.7044	Intermediate Similarity	NPC64391
0.7041	Intermediate Similarity	NPC477697
0.7041	Intermediate Similarity	NPC273657
0.7041	Intermediate Similarity	NPC106920
0.7041	Intermediate Similarity	NPC477696
0.7041	Intermediate Similarity	NPC49108
0.7041	Intermediate Similarity	NPC470811
0.7039	Intermediate Similarity	NPC474239
0.7037	Intermediate Similarity	NPC280399

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 NPC3906 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	184
0.1-0.2	737
0.2-0.3	1263
0.3-0.4	2622
0.4-0.5	2421
0.5-0.6	1404
0.6-0.7	498
0.7-0.8	18
0.8-0.85	1
0.85-0.9	2
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.9161	High Similarity	NPD5090	Approved
0.9161	High Similarity	NPD5089	Approved
0.8344	Intermediate Similarity	NPD4585	Approved
0.7765	Intermediate Similarity	NPD4055	Discovery
0.768	Intermediate Similarity	NPD6843	Phase 3
0.768	Intermediate Similarity	NPD6842	Approved
0.768	Intermediate Similarity	NPD6841	Approved
0.756	Intermediate Similarity	NPD4005	Discontinued
0.7365	Intermediate Similarity	NPD4357	Discontinued
0.7356	Intermediate Similarity	NPD7975	Clinical (unspecified phase)
0.7268	Intermediate Similarity	NPD3534	Clinical (unspecified phase)
0.7235	Intermediate Similarity	NPD3639	Approved
0.7235	Intermediate Similarity	NPD3640	Phase 3
0.7235	Intermediate Similarity	NPD3641	Approved
0.7126	Intermediate Similarity	NPD2654	Approved
0.7102	Intermediate Similarity	NPD3882	Suspended
0.7095	Intermediate Similarity	NPD7315	Approved
0.7081	Intermediate Similarity	NPD2968	Approved
0.7081	Intermediate Similarity	NPD2971	Approved
0.7056	Intermediate Similarity	NPD5242	Approved
0.7031	Intermediate Similarity	NPD2974	Approved
0.7031	Intermediate Similarity	NPD2975	Approved
0.7031	Intermediate Similarity	NPD2973	Approved
0.703	Intermediate Similarity	NPD6111	Discontinued
0.701	Intermediate Similarity	NPD4580	Approved
0.7	Intermediate Similarity	NPD7296	Approved
0.6977	Remote Similarity	NPD7527	Clinical (unspecified phase)
0.6977	Remote Similarity	NPD7526	Approved
0.6977	Remote Similarity	NPD52	Approved
0.6975	Remote Similarity	NPD2669	Clinical (unspecified phase)
0.6961	Remote Similarity	NPD7184	Clinical (unspecified phase)
0.6952	Remote Similarity	NPD7090	Clinical (unspecified phase)
0.6949	Remote Similarity	NPD3817	Phase 2
0.6949	Remote Similarity	NPD5978	Approved
0.6949	Remote Similarity	NPD5977	Approved
0.6947	Remote Similarity	NPD2488	Approved
0.6947	Remote Similarity	NPD2490	Approved
0.6946	Remote Similarity	NPD2161	Phase 2
0.6941	Remote Similarity	NPD2219	Phase 1
0.6939	Remote Similarity	NPD3057	Approved
0.6932	Remote Similarity	NPD37	Approved
0.6923	Remote Similarity	NPD4107	Approved
0.6914	Remote Similarity	NPD6876	Approved
0.6914	Remote Similarity	NPD6875	Approved
0.6905	Remote Similarity	NPD1375	Discontinued
0.6901	Remote Similarity	NPD7124	Phase 2
0.689	Remote Similarity	NPD2674	Phase 3
0.6889	Remote Similarity	NPD6746	Phase 2
0.6888	Remote Similarity	NPD3450	Approved
0.6888	Remote Similarity	NPD2493	Approved
0.6888	Remote Similarity	NPD2494	Approved
0.6888	Remote Similarity	NPD3452	Approved
0.6881	Remote Similarity	NPD7827	Phase 1
0.6875	Remote Similarity	NPD6385	Approved
0.6875	Remote Similarity	NPD6386	Approved
0.6869	Remote Similarity	NPD4582	Approved
0.6869	Remote Similarity	NPD4583	Approved
0.686	Remote Similarity	NPD5297	Approved
0.6859	Remote Similarity	NPD5525	Clinical (unspecified phase)
0.6854	Remote Similarity	NPD5353	Approved
0.6853	Remote Similarity	NPD5005	Approved
0.6853	Remote Similarity	NPD5006	Approved
0.6853	Remote Similarity	NPD2972	Approved
0.6853	Remote Similarity	NPD3533	Approved
0.6848	Remote Similarity	NPD2163	Approved
0.6842	Remote Similarity	NPD5307	Clinical (unspecified phase)
0.6839	Remote Similarity	NPD6980	Clinical (unspecified phase)
0.6831	Remote Similarity	NPD2898	Approved
0.6829	Remote Similarity	NPD3144	Approved
0.6829	Remote Similarity	NPD3145	Approved
0.6818	Remote Similarity	NPD4002	Approved
0.6818	Remote Similarity	NPD4678	Approved
0.6818	Remote Similarity	NPD4004	Approved
0.6818	Remote Similarity	NPD4675	Approved
0.6816	Remote Similarity	NPD4966	Approved
0.6816	Remote Similarity	NPD4965	Approved
0.6816	Remote Similarity	NPD5019	Clinical (unspecified phase)
0.6816	Remote Similarity	NPD4967	Phase 2
0.6802	Remote Similarity	NPD4482	Phase 3
0.6796	Remote Similarity	NPD5494	Approved
0.6793	Remote Similarity	NPD7473	Discontinued
0.6786	Remote Similarity	NPD7237	Clinical (unspecified phase)
0.6784	Remote Similarity	NPD6658	Clinical (unspecified phase)
0.6784	Remote Similarity	NPD6331	Phase 2
0.6782	Remote Similarity	NPD5261	Clinical (unspecified phase)
0.6782	Remote Similarity	NPD3647	Clinical (unspecified phase)
0.6776	Remote Similarity	NPD3926	Phase 2
0.6766	Remote Similarity	NPD1772	Clinical (unspecified phase)
0.6766	Remote Similarity	NPD2157	Approved
0.6765	Remote Similarity	NPD970	Clinical (unspecified phase)
0.6765	Remote Similarity	NPD4664	Clinical (unspecified phase)
0.6763	Remote Similarity	NPD6799	Approved
0.676	Remote Similarity	NPD2560	Approved
0.676	Remote Similarity	NPD2563	Approved
0.6758	Remote Similarity	NPD7199	Phase 2
0.6757	Remote Similarity	NPD8099	Discontinued
0.6757	Remote Similarity	NPD8252	Approved
0.6757	Remote Similarity	NPD8251	Approved
0.6755	Remote Similarity	NPD4419	Clinical (unspecified phase)
0.6751	Remote Similarity	NPD7501	Clinical (unspecified phase)
0.6748	Remote Similarity	NPD1712	Approved
0.6743	Remote Similarity	NPD6662	Clinical (unspecified phase)
0.6742	Remote Similarity	NPD1934	Approved
0.674	Remote Similarity	NPD919	Approved
0.674	Remote Similarity	NPD6234	Discontinued
0.6735	Remote Similarity	NPD4420	Approved
0.6727	Remote Similarity	NPD5109	Approved
0.6727	Remote Similarity	NPD5110	Phase 2
0.6727	Remote Similarity	NPD5111	Phase 2
0.6724	Remote Similarity	NPD3146	Approved
0.6724	Remote Similarity	NPD3688	Clinical (unspecified phase)
0.6724	Remote Similarity	NPD4584	Approved
0.6723	Remote Similarity	NPD6599	Discontinued
0.6721	Remote Similarity	NPD6232	Discontinued
0.672	Remote Similarity	NPD8156	Discontinued
0.6708	Remote Similarity	NPD1669	Approved
0.6704	Remote Similarity	NPD7972	Discontinued
0.6704	Remote Similarity	NPD2801	Approved
0.6704	Remote Similarity	NPD5773	Approved
0.6704	Remote Similarity	NPD5772	Approved
0.6702	Remote Similarity	NPD3658	Clinical (unspecified phase)
0.6699	Remote Similarity	NPD7907	Approved
0.6686	Remote Similarity	NPD651	Clinical (unspecified phase)
0.6685	Remote Similarity	NPD6873	Phase 2
0.6685	Remote Similarity	NPD7110	Phase 1
0.6685	Remote Similarity	NPD7109	Clinical (unspecified phase)
0.6685	Remote Similarity	NPD6971	Discontinued
0.6684	Remote Similarity	NPD8053	Approved
0.6684	Remote Similarity	NPD8054	Approved
0.6683	Remote Similarity	NPD4665	Approved
0.6683	Remote Similarity	NPD2491	Approved
0.6683	Remote Similarity	NPD3448	Approved
0.6667	Remote Similarity	NPD7291	Discontinued
0.6667	Remote Similarity	NPD1247	Approved
0.6667	Remote Similarity	NPD3473	Clinical (unspecified phase)
0.6667	Remote Similarity	NPD7549	Discontinued
0.6667	Remote Similarity	NPD5676	Approved
0.6649	Remote Similarity	NPD8055	Clinical (unspecified phase)
0.6649	Remote Similarity	NPD6167	Clinical (unspecified phase)
0.6649	Remote Similarity	NPD4481	Phase 3
0.6649	Remote Similarity	NPD6166	Phase 2
0.6649	Remote Similarity	NPD6168	Clinical (unspecified phase)
0.6633	Remote Similarity	NPD7667	Clinical (unspecified phase)
0.6631	Remote Similarity	NPD5844	Phase 1
0.663	Remote Similarity	NPD6788	Approved
0.663	Remote Similarity	NPD3051	Approved
0.6629	Remote Similarity	NPD4739	Approved
0.6628	Remote Similarity	NPD4236	Phase 3
0.6628	Remote Similarity	NPD4237	Approved
0.6611	Remote Similarity	NPD2393	Clinical (unspecified phase)
0.6611	Remote Similarity	NPD7819	Suspended
0.6611	Remote Similarity	NPD7096	Clinical (unspecified phase)
0.6605	Remote Similarity	NPD3676	Clinical (unspecified phase)
0.6603	Remote Similarity	NPD4111	Phase 1
0.6595	Remote Similarity	NPD2970	Approved
0.6595	Remote Similarity	NPD2969	Approved
0.6592	Remote Similarity	NPD7615	Clinical (unspecified phase)
0.6591	Remote Similarity	NPD1512	Approved
0.659	Remote Similarity	NPD4109	Clinical (unspecified phase)
0.659	Remote Similarity	NPD3750	Approved
0.659	Remote Similarity	NPD6398	Clinical (unspecified phase)
0.659	Remote Similarity	NPD4110	Phase 3
0.6588	Remote Similarity	NPD3748	Approved
0.6582	Remote Similarity	NPD5536	Phase 2
0.6576	Remote Similarity	NPD2821	Approved
0.6573	Remote Similarity	NPD7261	Clinical (unspecified phase)
0.6571	Remote Similarity	NPD7837	Clinical (unspecified phase)
0.657	Remote Similarity	NPD3655	Clinical (unspecified phase)
0.657	Remote Similarity	NPD7153	Discontinued
0.657	Remote Similarity	NPD7596	Clinical (unspecified phase)
0.6566	Remote Similarity	NPD3027	Phase 3
0.6566	Remote Similarity	NPD1024	Discontinued
0.6561	Remote Similarity	NPD7993	Clinical (unspecified phase)
0.6559	Remote Similarity	NPD7784	Clinical (unspecified phase)
0.6552	Remote Similarity	NPD5241	Discontinued
0.655	Remote Similarity	NPD6100	Approved
0.655	Remote Similarity	NPD6099	Approved
0.6548	Remote Similarity	NPD2238	Phase 2
0.6548	Remote Similarity	NPD1240	Approved
0.6545	Remote Similarity	NPD3018	Phase 2
0.6545	Remote Similarity	NPD7280	Phase 3
0.6545	Remote Similarity	NPD7281	Phase 3
0.6543	Remote Similarity	NPD5312	Approved
0.6543	Remote Similarity	NPD5313	Approved
0.6541	Remote Similarity	NPD5711	Approved
0.6541	Remote Similarity	NPD4166	Phase 2
0.6541	Remote Similarity	NPD4606	Clinical (unspecified phase)
0.6541	Remote Similarity	NPD5710	Approved
0.6541	Remote Similarity	NPD6071	Discontinued
0.6538	Remote Similarity	NPD4868	Clinical (unspecified phase)
0.6536	Remote Similarity	NPD6502	Phase 2
0.6535	Remote Similarity	NPD4040	Phase 1
0.6534	Remote Similarity	NPD1424	Approved
0.6534	Remote Similarity	NPD4123	Phase 3
0.6534	Remote Similarity	NPD2532	Approved
0.6534	Remote Similarity	NPD2533	Approved
0.6534	Remote Similarity	NPD2534	Approved
0.6534	Remote Similarity	NPD4378	Clinical (unspecified phase)
0.6526	Remote Similarity	NPD6104	Discontinued
0.6524	Remote Similarity	NPD3489	Phase 3

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