NPASS Compound

Structure

NPC29531 OpenBabel07101719152D 57 61 0 0 1 0 0 0 0 0999 V2000 2.7873 3.3218 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0898 1.4152 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7873 -4.3048 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.5427 -1.1537 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9680 0.1707 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3362 -3.4126 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 11.1974 -0.4322 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9391 0.6646 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7923 -0.4322 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.6436 -1.9067 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7499 -1.3908 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5626 -2.1407 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.6436 0.0593 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.4949 -1.4152 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4903 -0.7242 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1510 -1.6108 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0898 -2.3981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0220 -2.3026 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0220 1.3196 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2784 1.9078 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5626 1.1577 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7873 2.3389 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 5.2385 0.9237 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.7873 -3.3218 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 7.7923 -1.4152 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8095 -2.3853 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8095 1.4024 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.4949 -0.4322 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4731 -0.8874 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2385 -1.9067 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.3362 0.9237 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.3362 -1.9067 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.9659 1.8562 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1510 0.6278 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3542 1.2866 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7554 2.1682 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9680 1.6767 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6066 -2.6596 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.5747 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8193 -3.1511 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.9830 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8193 2.1682 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 4.6066 1.6767 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 3.7554 -3.1511 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 5.5747 -0.9830 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 0.9680 -2.6596 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 3.4574 2.7075 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.0916 3.0919 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.3362 2.4297 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.2385 -3.4126 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.5427 0.1707 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.4831 -4.0748 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.9680 -1.1537 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 10.3461 0.0593 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.3262 1.4331 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4731 -0.0956 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4 45 1 0 0 0 0 5 46 1 0 0 0 0 6 47 1 0 0 0 0 7 55 1 0 0 0 0 8 56 1 0 0 0 0 9 13 1 0 0 0 0 9 25 2 0 0 0 0 10 14 2 0 0 0 0 10 25 1 0 0 0 0 11 15 1 0 0 0 0 11 26 2 0 0 0 0 12 16 2 0 0 0 0 12 26 1 0 0 0 0 13 28 2 0 0 0 0 14 28 1 0 0 0 0 15 29 2 0 0 0 0 16 29 1 0 0 0 0 17 25 1 0 0 0 0 18 26 1 0 0 0 0 19 27 1 0 0 0 0 20 27 2 0 0 0 0 20 33 1 0 0 0 0 21 27 1 0 0 0 0 21 34 2 0 0 0 0 22 1 1 6 0 0 0 22 36 1 0 0 0 0 22 42 1 0 0 0 0 23 2 1 1 0 0 0 23 39 1 0 0 0 0 23 43 1 0 0 0 0 24 3 1 1 0 0 0 24 40 1 0 0 0 0 24 44 1 0 0 0 0 28 55 1 0 0 0 0 29 57 1 0 0 0 0 30 17 1 1 0 0 0 30 38 1 0 0 0 0 30 45 1 0 0 0 0 31 19 1 1 0 0 0 31 37 1 0 0 0 0 31 46 1 0 0 0 0 32 18 1 1 0 0 0 32 41 1 0 0 0 0 32 47 1 0 0 0 0 33 35 2 0 0 0 0 33 48 1 0 0 0 0 34 35 1 0 0 0 0 34 57 1 0 0 0 0 35 56 1 0 0 0 0 36 43 2 3 0 0 0 36 49 1 0 0 0 0 37 42 2 3 0 0 0 37 50 1 0 0 0 0 38 44 2 3 0 0 0 38 51 1 0 0 0 0 39 45 1 0 0 0 0 39 52 2 0 0 0 0 40 47 1 0 0 0 0 40 53 2 0 0 0 0 41 46 1 0 0 0 0 41 54 2 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	786.36
Volume:	789.246
LogP:	2.111
LogD:	1.802
LogS:	-3.862
# Rotatable Bonds:	4
TPSA:	196.15
# H-Bond Aceptor:	16
# H-Bond Donor:	4
# Rings:	6
# Heavy Atoms:	16

MedChem Properties

QED Drug-Likeness Score:	0.302
Synthetic Accessibility Score:	6.667
Fsp3:	0.415
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	1
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.587
MDCK Permeability:	1.992078250623308e-05
Pgp-inhibitor:	1.0
Pgp-substrate:	0.728
Human Intestinal Absorption (HIA):	0.195
20% Bioavailability (F20%):	0.056
30% Bioavailability (F30%):	0.675

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.056
Plasma Protein Binding (PPB):	70.58694458007812%
Volume Distribution (VD):	0.263
Pgp-substrate:	16.92784881591797%

ADMET: Metabolism

CYP1A2-inhibitor:	0.003
CYP1A2-substrate:	0.053
CYP2C19-inhibitor:	0.139
CYP2C19-substrate:	0.089
CYP2C9-inhibitor:	0.277
CYP2C9-substrate:	0.067
CYP2D6-inhibitor:	0.021
CYP2D6-substrate:	0.262
CYP3A4-inhibitor:	0.942
CYP3A4-substrate:	0.142

ADMET: Excretion

Clearance (CL):	8.512
Half-life (T1/2):	0.223

ADMET: Toxicity

hERG Blockers:	0.029
Human Hepatotoxicity (H-HT):	0.976
Drug-inuced Liver Injury (DILI):	0.952
AMES Toxicity:	0.024
Rat Oral Acute Toxicity:	0.427
Maximum Recommended Daily Dose:	0.933
Skin Sensitization:	0.034
Carcinogencity:	0.017
Eye Corrosion:	0.003
Eye Irritation:	0.004
Respiratory Toxicity:	0.233

Download Data

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

Natural Product: NPC29531

Natural Product ID:	NPC29531
*Common Name:**	JEBXCSWDHPJRMW-LZQLRFBTSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	JEBXCSWDHPJRMW-LZQLRFBTSA-N
Standard InCHI:	InChI=1S/C41H50N6O10/c1-22-36(49)43-23(2)39(52)45(4)30(17-25-9-13-28(55-7)14-10-25)38(51)44-24(3)40(53)47(6)32-18-26-11-15-29(16-12-26)57-34-21-27(20-33(48)35(34)56-8)19-31(37(50)42-22)46(5)41(32)54/h9-16,20-24,30-32,48H,17-19H2,1-8H3,(H,42,50)(H,43,49)(H,44,51)/t22-,23+,24+,30+,31+,32+/m1/s1
SMILES:	COc1ccc(cc1)C[C@H]1C(=N[C@@H](C)C(=O)N(C)[C@H]2Cc3ccc(cc3)Oc3cc(C[C@H](N(C2=O)C)C(=N[C@@H](C(=N[C@H](C(=O)N1C)C)O)C)O)cc(c3OC)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL404614
PubChem CID:	25033039
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000264] Organic acids and derivatives [CHEMONTID:0000265] Carboxylic acids and derivatives [CHEMONTID:0000013] Amino acids, peptides, and analogues [CHEMONTID:0000348] Peptides [CHEMONTID:0004831] Oligopeptides

*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
NPO26542	Rubia cordifolia	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18078747]
NPO26542	Rubia cordifolia	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[8882438]
NPO26542	Rubia cordifolia	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO26542	Rubia cordifolia	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO26542	Rubia cordifolia	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO26542	Rubia cordifolia	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO26542	Rubia cordifolia	Species	Rubiaceae	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
IC50	1

Activity Type	# Activity
Cell Line	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT168	Cell Line	P388	Mus musculus	IC50	=	0.012	ug.mL-1	PMID[505149]

☑ 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 NPC29531 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	279
0.1-0.2	1438
0.2-0.3	7519
0.3-0.4	10453
0.4-0.5	5897
0.5-0.6	9485
0.6-0.7	7186
0.7-0.8	421
0.8-0.85	4
0.85-0.9	4
0.9-0.95	8
0.95-1	3

Similarity Score	Similarity Level	Natural Product ID
0.954	High Similarity	NPC471563
0.9524	High Similarity	NPC32064
0.9302	High Similarity	NPC138083
0.9286	High Similarity	NPC164608
0.9249	High Similarity	NPC276120
0.9091	High Similarity	NPC174122
0.9091	High Similarity	NPC64140
0.9056	High Similarity	NPC50548
0.9034	High Similarity	NPC234069
0.9	High Similarity	NPC144314
0.8944	High Similarity	NPC149962
0.8798	High Similarity	NPC123859
0.875	High Similarity	NPC242728
0.8125	Intermediate Similarity	NPC473460
0.8083	Intermediate Similarity	NPC473422
0.804	Intermediate Similarity	NPC471531
0.8023	Intermediate Similarity	NPC127402
0.8	Intermediate Similarity	NPC281629
0.7926	Intermediate Similarity	NPC473407
0.7926	Intermediate Similarity	NPC473378
0.7919	Intermediate Similarity	NPC471561
0.7886	Intermediate Similarity	NPC107602
0.7884	Intermediate Similarity	NPC41122
0.7884	Intermediate Similarity	NPC318805
0.7876	Intermediate Similarity	NPC469689
0.7876	Intermediate Similarity	NPC471031
0.7865	Intermediate Similarity	NPC50380
0.7865	Intermediate Similarity	NPC179250
0.7849	Intermediate Similarity	NPC315542
0.7839	Intermediate Similarity	NPC471532
0.7829	Intermediate Similarity	NPC56635
0.7784	Intermediate Similarity	NPC287757
0.7784	Intermediate Similarity	NPC319320
0.7765	Intermediate Similarity	NPC254700
0.7754	Intermediate Similarity	NPC30779
0.7746	Intermediate Similarity	NPC233702
0.772	Intermediate Similarity	NPC234318
0.7708	Intermediate Similarity	NPC85381
0.7705	Intermediate Similarity	NPC155506
0.7705	Intermediate Similarity	NPC159767
0.7701	Intermediate Similarity	NPC286119
0.7692	Intermediate Similarity	NPC475654
0.7674	Intermediate Similarity	NPC5462
0.766	Intermediate Similarity	NPC49075
0.766	Intermediate Similarity	NPC222661
0.766	Intermediate Similarity	NPC258657
0.766	Intermediate Similarity	NPC271013
0.766	Intermediate Similarity	NPC182052
0.766	Intermediate Similarity	NPC279228
0.766	Intermediate Similarity	NPC328155
0.766	Intermediate Similarity	NPC104196
0.766	Intermediate Similarity	NPC15414
0.766	Intermediate Similarity	NPC54654
0.766	Intermediate Similarity	NPC251735
0.766	Intermediate Similarity	NPC90998
0.766	Intermediate Similarity	NPC290005
0.766	Intermediate Similarity	NPC42663
0.766	Intermediate Similarity	NPC7715
0.766	Intermediate Similarity	NPC285931
0.766	Intermediate Similarity	NPC229373
0.766	Intermediate Similarity	NPC290582
0.766	Intermediate Similarity	NPC239824
0.766	Intermediate Similarity	NPC223690
0.766	Intermediate Similarity	NPC217748
0.766	Intermediate Similarity	NPC311973
0.766	Intermediate Similarity	NPC185639
0.766	Intermediate Similarity	NPC181796
0.766	Intermediate Similarity	NPC8836
0.7637	Intermediate Similarity	NPC196091
0.7633	Intermediate Similarity	NPC296898
0.7626	Intermediate Similarity	NPC477666
0.7619	Intermediate Similarity	NPC254441
0.7619	Intermediate Similarity	NPC274716
0.7619	Intermediate Similarity	NPC167116
0.7616	Intermediate Similarity	NPC16188
0.761	Intermediate Similarity	NPC82056
0.7609	Intermediate Similarity	NPC476227
0.7609	Intermediate Similarity	NPC26108
0.7609	Intermediate Similarity	NPC473402
0.7609	Intermediate Similarity	NPC473354
0.7606	Intermediate Similarity	NPC294951
0.7596	Intermediate Similarity	NPC230611
0.7594	Intermediate Similarity	NPC329816
0.7586	Intermediate Similarity	NPC277857
0.7586	Intermediate Similarity	NPC115144
0.7581	Intermediate Similarity	NPC45037
0.7554	Intermediate Similarity	NPC204908
0.7554	Intermediate Similarity	NPC83198
0.7554	Intermediate Similarity	NPC306804
0.7554	Intermediate Similarity	NPC273755
0.7553	Intermediate Similarity	NPC471526
0.7543	Intermediate Similarity	NPC470935
0.7543	Intermediate Similarity	NPC471032
0.7539	Intermediate Similarity	NPC124626
0.7539	Intermediate Similarity	NPC212237
0.7539	Intermediate Similarity	NPC116465
0.7528	Intermediate Similarity	NPC475557
0.7527	Intermediate Similarity	NPC107938
0.7527	Intermediate Similarity	NPC294516
0.7525	Intermediate Similarity	NPC311357
0.7513	Intermediate Similarity	NPC195538
0.75	Intermediate Similarity	NPC202198
0.75	Intermediate Similarity	NPC22115
0.75	Intermediate Similarity	NPC275680
0.75	Intermediate Similarity	NPC89831
0.7486	Intermediate Similarity	NPC186617
0.7486	Intermediate Similarity	NPC324081
0.7474	Intermediate Similarity	NPC476202
0.7471	Intermediate Similarity	NPC9373
0.7461	Intermediate Similarity	NPC175890
0.7461	Intermediate Similarity	NPC82457
0.7461	Intermediate Similarity	NPC274661
0.7461	Intermediate Similarity	NPC206900
0.7461	Intermediate Similarity	NPC11296
0.7461	Intermediate Similarity	NPC48490
0.7459	Intermediate Similarity	NPC137627
0.7459	Intermediate Similarity	NPC473748
0.7446	Intermediate Similarity	NPC473693
0.7446	Intermediate Similarity	NPC90984
0.7446	Intermediate Similarity	NPC471568
0.7436	Intermediate Similarity	NPC478092
0.7436	Intermediate Similarity	NPC30182
0.7436	Intermediate Similarity	NPC473589
0.7436	Intermediate Similarity	NPC478091
0.7433	Intermediate Similarity	NPC232386
0.7433	Intermediate Similarity	NPC152680
0.7433	Intermediate Similarity	NPC190783
0.7432	Intermediate Similarity	NPC141957
0.7432	Intermediate Similarity	NPC328649
0.7427	Intermediate Similarity	NPC38964
0.7423	Intermediate Similarity	NPC60295
0.7423	Intermediate Similarity	NPC191132
0.7419	Intermediate Similarity	NPC279871
0.7419	Intermediate Similarity	NPC471165
0.7418	Intermediate Similarity	NPC472923
0.7409	Intermediate Similarity	NPC163961
0.7409	Intermediate Similarity	NPC473305
0.7407	Intermediate Similarity	NPC476321
0.7399	Intermediate Similarity	NPC222039
0.7399	Intermediate Similarity	NPC100478
0.7396	Intermediate Similarity	NPC249996
0.7396	Intermediate Similarity	NPC16357
0.7396	Intermediate Similarity	NPC302245
0.7396	Intermediate Similarity	NPC95426
0.7394	Intermediate Similarity	NPC194671
0.7394	Intermediate Similarity	NPC269750
0.7385	Intermediate Similarity	NPC478093
0.7385	Intermediate Similarity	NPC24260
0.738	Intermediate Similarity	NPC50016
0.7377	Intermediate Similarity	NPC304074
0.7377	Intermediate Similarity	NPC471771
0.7377	Intermediate Similarity	NPC290755
0.7366	Intermediate Similarity	NPC477665
0.7363	Intermediate Similarity	NPC329837
0.7358	Intermediate Similarity	NPC65312
0.7358	Intermediate Similarity	NPC139783
0.7351	Intermediate Similarity	NPC42549
0.7351	Intermediate Similarity	NPC268503
0.7351	Intermediate Similarity	NPC264850
0.7351	Intermediate Similarity	NPC329717
0.7351	Intermediate Similarity	NPC317272
0.7351	Intermediate Similarity	NPC474858
0.7351	Intermediate Similarity	NPC40234
0.7351	Intermediate Similarity	NPC13916
0.7351	Intermediate Similarity	NPC256012
0.7351	Intermediate Similarity	NPC240841
0.7351	Intermediate Similarity	NPC250846
0.7346	Intermediate Similarity	NPC475349
0.7346	Intermediate Similarity	NPC475565
0.7346	Intermediate Similarity	NPC475292
0.7333	Intermediate Similarity	NPC475597
0.7333	Intermediate Similarity	NPC473716
0.733	Intermediate Similarity	NPC473562
0.733	Intermediate Similarity	NPC245974
0.733	Intermediate Similarity	NPC471048
0.733	Intermediate Similarity	NPC471050
0.733	Intermediate Similarity	NPC471049
0.7326	Intermediate Similarity	NPC476989
0.7326	Intermediate Similarity	NPC299583
0.7322	Intermediate Similarity	NPC223207
0.7321	Intermediate Similarity	NPC114102
0.7314	Intermediate Similarity	NPC247298
0.7311	Intermediate Similarity	NPC475624
0.7304	Intermediate Similarity	NPC293347
0.7303	Intermediate Similarity	NPC262166
0.7302	Intermediate Similarity	NPC475421
0.7299	Intermediate Similarity	NPC470846
0.7297	Intermediate Similarity	NPC24465
0.7291	Intermediate Similarity	NPC79130
0.7288	Intermediate Similarity	NPC473491
0.7287	Intermediate Similarity	NPC198498
0.7287	Intermediate Similarity	NPC276890
0.7287	Intermediate Similarity	NPC196243
0.7287	Intermediate Similarity	NPC115284
0.7287	Intermediate Similarity	NPC317439
0.7287	Intermediate Similarity	NPC76682
0.7287	Intermediate Similarity	NPC317145
0.7287	Intermediate Similarity	NPC227060
0.7287	Intermediate Similarity	NPC63646
0.7287	Intermediate Similarity	NPC10908

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 NPC29531 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	172
0.1-0.2	570
0.2-0.3	1229
0.3-0.4	2036
0.4-0.5	2520
0.5-0.6	1921
0.6-0.7	647
0.7-0.8	55
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
0.7935	Intermediate Similarity	NPD7132	Clinical (unspecified phase)
0.7907	Intermediate Similarity	NPD7131	Phase 3
0.774	Intermediate Similarity	NPD5773	Approved
0.774	Intermediate Similarity	NPD5772	Approved
0.7719	Intermediate Similarity	NPD2219	Phase 1
0.767	Intermediate Similarity	NPD4678	Approved
0.767	Intermediate Similarity	NPD4675	Approved
0.7668	Intermediate Similarity	NPD7667	Clinical (unspecified phase)
0.766	Intermediate Similarity	NPD8054	Approved
0.766	Intermediate Similarity	NPD6851	Approved
0.766	Intermediate Similarity	NPD8053	Approved
0.766	Intermediate Similarity	NPD6853	Approved
0.766	Intermediate Similarity	NPD7090	Clinical (unspecified phase)
0.7634	Intermediate Similarity	NPD6297	Approved
0.7602	Intermediate Similarity	NPD7501	Clinical (unspecified phase)
0.7592	Intermediate Similarity	NPD6377	Clinical (unspecified phase)
0.7541	Intermediate Similarity	NPD7608	Discontinued
0.7537	Intermediate Similarity	NPD7827	Phase 1
0.7514	Intermediate Similarity	NPD7975	Clinical (unspecified phase)
0.7444	Intermediate Similarity	NPD6818	Clinical (unspecified phase)
0.7432	Intermediate Similarity	NPD5677	Discontinued
0.7391	Intermediate Similarity	NPD7484	Phase 3
0.7391	Intermediate Similarity	NPD7485	Phase 3
0.7386	Intermediate Similarity	NPD4123	Phase 3
0.7348	Intermediate Similarity	NPD7046	Clinical (unspecified phase)
0.733	Intermediate Similarity	NPD7281	Phase 3
0.733	Intermediate Similarity	NPD7280	Phase 3
0.7318	Intermediate Similarity	NPD4005	Discontinued
0.7316	Intermediate Similarity	NPD7038	Approved
0.7316	Intermediate Similarity	NPD7039	Approved
0.7312	Intermediate Similarity	NPD5137	Approved
0.7303	Intermediate Similarity	NPD6662	Clinical (unspecified phase)
0.7291	Intermediate Similarity	NPD7263	Phase 2
0.7287	Intermediate Similarity	NPD8099	Discontinued
0.7287	Intermediate Similarity	NPD8251	Approved
0.7287	Intermediate Similarity	NPD8252	Approved
0.7286	Intermediate Similarity	NPD7811	Phase 3
0.7286	Intermediate Similarity	NPD7810	Phase 3
0.7282	Intermediate Similarity	NPD5525	Clinical (unspecified phase)
0.7268	Intermediate Similarity	NPD7906	Approved
0.7249	Intermediate Similarity	NPD8156	Discontinued
0.7243	Intermediate Similarity	NPD6746	Phase 2
0.7238	Intermediate Similarity	NPD7110	Phase 1
0.7238	Intermediate Similarity	NPD7109	Clinical (unspecified phase)
0.7232	Intermediate Similarity	NPD5297	Approved
0.7222	Intermediate Similarity	NPD7261	Clinical (unspecified phase)
0.7216	Intermediate Similarity	NPD5241	Discontinued
0.7214	Intermediate Similarity	NPD2493	Approved
0.7214	Intermediate Similarity	NPD2494	Approved
0.7207	Intermediate Similarity	NPD2122	Discontinued
0.7198	Intermediate Similarity	NPD7945	Clinical (unspecified phase)
0.7191	Intermediate Similarity	NPD7447	Phase 1
0.7179	Intermediate Similarity	NPD7291	Discontinued
0.7175	Intermediate Similarity	NPD7124	Phase 2
0.7174	Intermediate Similarity	NPD6788	Approved
0.7158	Intermediate Similarity	NPD6668	Clinical (unspecified phase)
0.7151	Intermediate Similarity	NPD7201	Clinical (unspecified phase)
0.7143	Intermediate Similarity	NPD7118	Clinical (unspecified phase)
0.7143	Intermediate Similarity	NPD6072	Discontinued
0.7143	Intermediate Similarity	NPD7596	Clinical (unspecified phase)
0.7135	Intermediate Similarity	NPD4357	Discontinued
0.7129	Intermediate Similarity	NPD3450	Approved
0.7129	Intermediate Similarity	NPD3452	Approved
0.7118	Intermediate Similarity	NPD5718	Phase 2
0.7108	Intermediate Similarity	NPD4582	Approved
0.7108	Intermediate Similarity	NPD4583	Approved
0.7102	Intermediate Similarity	NPD3060	Approved
0.7101	Intermediate Similarity	NPD5752	Clinical (unspecified phase)
0.7098	Intermediate Similarity	NPD4419	Clinical (unspecified phase)
0.7095	Intermediate Similarity	NPD3146	Approved
0.7095	Intermediate Similarity	NPD1754	Clinical (unspecified phase)
0.7095	Intermediate Similarity	NPD3688	Clinical (unspecified phase)
0.7095	Intermediate Similarity	NPD7047	Phase 3
0.7088	Intermediate Similarity	NPD6875	Approved
0.7088	Intermediate Similarity	NPD6876	Approved
0.7085	Intermediate Similarity	NPD4413	Clinical (unspecified phase)
0.7068	Intermediate Similarity	NPD42	Phase 2
0.7068	Intermediate Similarity	NPD6042	Phase 2
0.7065	Intermediate Similarity	NPD2977	Approved
0.7065	Intermediate Similarity	NPD2978	Approved
0.7059	Intermediate Similarity	NPD4004	Approved
0.7059	Intermediate Similarity	NPD4002	Approved
0.7056	Intermediate Similarity	NPD7861	Discontinued
0.7049	Intermediate Similarity	NPD6386	Approved
0.7049	Intermediate Similarity	NPD6385	Approved
0.7039	Intermediate Similarity	NPD7213	Phase 3
0.7039	Intermediate Similarity	NPD7212	Phase 2
0.7033	Intermediate Similarity	NPD824	Approved
0.7029	Intermediate Similarity	NPD7450	Phase 2
0.7027	Intermediate Similarity	NPD5967	Approved
0.7022	Intermediate Similarity	NPD5307	Clinical (unspecified phase)
0.702	Intermediate Similarity	NPD2488	Approved
0.702	Intermediate Similarity	NPD2490	Approved
0.7015	Intermediate Similarity	NPD2975	Approved
0.7015	Intermediate Similarity	NPD2974	Approved
0.7015	Intermediate Similarity	NPD2973	Approved
0.7006	Intermediate Similarity	NPD4237	Approved
0.7006	Intermediate Similarity	NPD4162	Approved
0.7006	Intermediate Similarity	NPD4236	Phase 3
0.7005	Intermediate Similarity	NPD4157	Discontinued
0.7	Intermediate Similarity	NPD6312	Discontinued
0.699	Remote Similarity	NPD7607	Clinical (unspecified phase)
0.6978	Remote Similarity	NPD3686	Approved
0.6978	Remote Similarity	NPD3687	Approved
0.6977	Remote Similarity	NPD5745	Approved
0.6977	Remote Similarity	NPD6997	Phase 2
0.6977	Remote Similarity	NPD2674	Phase 3
0.6974	Remote Similarity	NPD4577	Approved
0.6974	Remote Similarity	NPD4578	Approved
0.6961	Remote Similarity	NPD7526	Approved
0.6961	Remote Similarity	NPD7527	Clinical (unspecified phase)
0.6961	Remote Similarity	NPD52	Approved
0.6954	Remote Similarity	NPD4663	Approved
0.6952	Remote Similarity	NPD6971	Discontinued
0.6952	Remote Similarity	NPD4055	Discovery
0.6952	Remote Similarity	NPD8031	Discontinued
0.6947	Remote Similarity	NPD5242	Approved
0.6934	Remote Similarity	NPD8149	Discontinued
0.6923	Remote Similarity	NPD7585	Approved
0.6919	Remote Similarity	NPD7243	Clinical (unspecified phase)
0.6919	Remote Similarity	NPD8019	Approved
0.6916	Remote Similarity	NPD8318	Clinical (unspecified phase)
0.6915	Remote Similarity	NPD3473	Clinical (unspecified phase)
0.6912	Remote Similarity	NPD4580	Approved
0.6885	Remote Similarity	NPD4210	Discontinued
0.6882	Remote Similarity	NPD7972	Discontinued
0.6882	Remote Similarity	NPD2801	Approved
0.6875	Remote Similarity	NPD7583	Approved
0.6872	Remote Similarity	NPD6331	Phase 2
0.6872	Remote Similarity	NPD6658	Clinical (unspecified phase)
0.6868	Remote Similarity	NPD5261	Clinical (unspecified phase)
0.6863	Remote Similarity	NPD7237	Clinical (unspecified phase)
0.6862	Remote Similarity	NPD8070	Approved
0.686	Remote Similarity	NPD5746	Approved
0.6859	Remote Similarity	NPD8051	Clinical (unspecified phase)
0.6854	Remote Similarity	NPD3655	Clinical (unspecified phase)
0.6854	Remote Similarity	NPD7153	Discontinued
0.685	Remote Similarity	NPD6504	Approved
0.685	Remote Similarity	NPD6505	Approved
0.6848	Remote Similarity	NPD8158	Clinical (unspecified phase)
0.6848	Remote Similarity	NPD3455	Phase 2
0.6837	Remote Similarity	NPD7549	Discontinued
0.6837	Remote Similarity	NPD3936	Clinical (unspecified phase)
0.6834	Remote Similarity	NPD4435	Approved
0.6833	Remote Similarity	NPD3692	Discontinued
0.6828	Remote Similarity	NPD1934	Approved
0.6826	Remote Similarity	NPD8153	Approved
0.6826	Remote Similarity	NPD8152	Approved
0.6823	Remote Similarity	NPD6168	Clinical (unspecified phase)
0.6823	Remote Similarity	NPD6166	Phase 2
0.6823	Remote Similarity	NPD6167	Clinical (unspecified phase)
0.6823	Remote Similarity	NPD2489	Approved
0.6823	Remote Similarity	NPD27	Approved
0.6821	Remote Similarity	NPD3145	Approved
0.6821	Remote Similarity	NPD3144	Approved
0.6821	Remote Similarity	NPD6996	Clinical (unspecified phase)
0.6816	Remote Similarity	NPD6860	Clinical (unspecified phase)
0.6813	Remote Similarity	NPD3157	Approved
0.6813	Remote Similarity	NPD3158	Phase 1
0.6813	Remote Similarity	NPD3536	Discontinued
0.6811	Remote Similarity	NPD6502	Phase 2
0.6809	Remote Similarity	NPD5019	Clinical (unspecified phase)
0.6809	Remote Similarity	NPD4868	Clinical (unspecified phase)
0.6806	Remote Similarity	NPD3051	Approved
0.6806	Remote Similarity	NPD2517	Approved
0.6806	Remote Similarity	NPD7315	Approved
0.6804	Remote Similarity	NPD5313	Approved
0.6804	Remote Similarity	NPD5312	Approved
0.6802	Remote Similarity	NPD7311	Approved
0.6802	Remote Similarity	NPD7312	Approved
0.6802	Remote Similarity	NPD7310	Approved
0.6802	Remote Similarity	NPD3534	Clinical (unspecified phase)
0.6802	Remote Similarity	NPD7313	Approved
0.6796	Remote Similarity	NPD6666	Approved
0.6796	Remote Similarity	NPD6667	Approved
0.6794	Remote Similarity	NPD7584	Approved
0.6786	Remote Similarity	NPD5192	Clinical (unspecified phase)
0.6784	Remote Similarity	NPD6584	Phase 3
0.6784	Remote Similarity	NPD4434	Approved
0.6782	Remote Similarity	NPD2245	Discovery
0.6779	Remote Similarity	NPD4040	Phase 1
0.6776	Remote Similarity	NPD1975	Clinical (unspecified phase)
0.6774	Remote Similarity	NPD5089	Approved
0.6774	Remote Similarity	NPD7615	Clinical (unspecified phase)
0.6774	Remote Similarity	NPD5090	Approved
0.6772	Remote Similarity	NPD7831	Phase 2
0.6772	Remote Similarity	NPD7832	Clinical (unspecified phase)
0.6772	Remote Similarity	NPD7833	Phase 2
0.6771	Remote Similarity	NPD2970	Approved
0.6771	Remote Similarity	NPD2969	Approved
0.6769	Remote Similarity	NPD5485	Approved
0.6769	Remote Similarity	NPD5484	Approved
0.6768	Remote Similarity	NPD7309	Approved
0.6763	Remote Similarity	NPD3027	Phase 3
0.676	Remote Similarity	NPD4664	Clinical (unspecified phase)
0.6757	Remote Similarity	NPD6523	Clinical (unspecified phase)
0.6755	Remote Similarity	NPD5353	Approved
0.6754	Remote Similarity	NPD2516	Approved
0.6753	Remote Similarity	NPD7177	Discontinued
0.6753	Remote Similarity	NPD5940	Clinical (unspecified phase)

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