NPASS Compound

Structure

NPC56635 OpenBabel07101718182D 54 57 0 0 1 0 0 0 0 0999 V2000 3.1221 -7.9397 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2561 -9.4397 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8356 3.3794 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8356 -4.3794 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1221 -0.0603 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2561 -0.5603 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1221 0.9397 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3900 -0.0603 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2561 1.4397 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.0613 -0.9397 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.9273 -2.4397 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3420 -3.9397 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3900 -3.9397 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.9273 -0.4397 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.7934 -1.9397 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3420 -4.9397 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3900 -4.9397 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3900 -7.9397 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3900 -6.9397 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.1953 -2.4397 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5240 -2.4397 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5240 1.4397 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.3293 0.9397 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2561 -8.4397 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8356 2.3794 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.8356 -3.3794 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.3900 0.9397 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.0613 -1.9397 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5240 -3.4397 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.7934 -0.9397 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5240 -5.4397 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.3293 -1.9397 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.3420 -1.9397 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.3420 0.9397 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.6713 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8204 2.2057 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8508 -3.2057 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.6865 -2.7057 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9848 1.7057 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 -4.6865 1.7057 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -3.8204 -3.2057 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -1.8508 2.2057 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -5.6713 -1.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -0.9848 -2.7057 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -9.6594 -0.4397 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.6561 0.1736 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.1625 3.1454 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.5088 -4.1454 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.3293 -3.4718 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.3420 2.4718 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.9848 -1.1736 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.5240 -6.4397 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 1 24 1 0 0 0 0 2 24 1 0 0 0 0 5 6 2 0 0 0 0 5 7 1 0 0 0 0 6 8 1 0 0 0 0 7 9 2 0 0 0 0 8 27 2 0 0 0 0 9 27 1 0 0 0 0 10 14 1 0 0 0 0 10 28 2 0 0 0 0 11 15 2 0 0 0 0 11 28 1 0 0 0 0 12 16 1 0 0 0 0 12 29 2 0 0 0 0 13 17 2 0 0 0 0 13 29 1 0 0 0 0 14 30 2 0 0 0 0 15 30 1 0 0 0 0 16 31 2 0 0 0 0 17 31 1 0 0 0 0 18 19 1 0 0 0 0 18 24 2 0 0 0 0 19 53 1 0 0 0 0 20 28 1 0 0 0 0 21 29 1 0 0 0 0 22 27 1 0 0 0 0 23 35 1 0 0 0 0 23 41 1 0 0 0 0 25 3 1 6 0 0 0 25 36 1 0 0 0 0 25 43 1 0 0 0 0 26 4 1 1 0 0 0 26 37 1 0 0 0 0 26 42 1 0 0 0 0 30 46 1 0 0 0 0 31 53 1 0 0 0 0 32 20 1 1 0 0 0 32 38 1 0 0 0 0 32 44 1 0 0 0 0 33 21 1 1 0 0 0 33 40 1 0 0 0 0 33 45 1 0 0 0 0 34 22 1 6 0 0 0 34 39 1 0 0 0 0 34 54 1 0 0 0 0 35 44 2 3 0 0 0 35 47 1 0 0 0 0 36 41 2 3 0 0 0 36 48 1 0 0 0 0 37 45 2 3 0 0 0 37 49 1 0 0 0 0 38 42 2 3 0 0 0 38 50 1 0 0 0 0 39 43 2 3 0 0 0 39 51 1 0 0 0 0 40 52 2 0 0 0 0 40 54 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	741.34
Volume:	758.083
LogP:	4.778
LogD:	3.567
LogS:	-4.446
# Rotatable Bonds:	9
TPSA:	201.26
# H-Bond Aceptor:	14
# H-Bond Donor:	6
# Rings:	4
# Heavy Atoms:	14

MedChem Properties

QED Drug-Likeness Score:	0.14
Synthetic Accessibility Score:	4.993
Fsp3:	0.35
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.558
MDCK Permeability:	8.042370609473437e-06
Pgp-inhibitor:	0.997
Pgp-substrate:	0.996
Human Intestinal Absorption (HIA):	0.022
20% Bioavailability (F20%):	0.874
30% Bioavailability (F30%):	0.998

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.012
Plasma Protein Binding (PPB):	95.9684829711914%
Volume Distribution (VD):	0.213
Pgp-substrate:	2.6894733905792236%

ADMET: Metabolism

CYP1A2-inhibitor:	0.004
CYP1A2-substrate:	0.009
CYP2C19-inhibitor:	0.322
CYP2C19-substrate:	0.045
CYP2C9-inhibitor:	0.623
CYP2C9-substrate:	0.09
CYP2D6-inhibitor:	0.015
CYP2D6-substrate:	0.18
CYP3A4-inhibitor:	0.879
CYP3A4-substrate:	0.064

ADMET: Excretion

Clearance (CL):	5.075
Half-life (T1/2):	0.226

ADMET: Toxicity

hERG Blockers:	0.362
Human Hepatotoxicity (H-HT):	0.98
Drug-inuced Liver Injury (DILI):	0.739
AMES Toxicity:	0.02
Rat Oral Acute Toxicity:	0.109
Maximum Recommended Daily Dose:	0.568
Skin Sensitization:	0.054
Carcinogencity:	0.016
Eye Corrosion:	0.003
Eye Irritation:	0.004
Respiratory Toxicity:	0.051

Download Data

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

Natural Product: NPC56635

Natural Product ID:	NPC56635
*Common Name:**	Paecilodepsipeptide A
IUPAC Name:	(3R,6R,9R,15S,18S)-18-benzyl-9-[(4-hydroxyphenyl)methyl]-6,15-dimethyl-3-[[4-(3-methylbut-2-enoxy)phenyl]methyl]-1-oxa-4,7,10,13,16-pentazacyclooctadecane-2,5,8,11,14,17-hexone
Synonyms:
Standard InCHIKey:	JNXJCUUDHZAFNN-ZIWQVPDVSA-N
Standard InCHI:	InChI=1S/C40H47N5O9/c1-24(2)18-19-53-31-16-12-29(13-17-31)21-33-40(52)54-34(22-27-8-6-5-7-9-27)39(51)43-25(3)36(48)41-23-35(47)44-32(20-28-10-14-30(46)15-11-28)38(50)42-26(4)37(49)45-33/h5-18,25-26,32-34,46H,19-23H2,1-4H3,(H,41,48)(H,42,50)(H,43,51)(H,44,47)(H,45,49)/t25-,26+,32+,33+,34-/m0/s1
SMILES:	CC(=CCOc1ccc(cc1)C[C@H]1N=C(O)[C@@H](C)N=C(O)[C@@H](Cc2ccc(cc2)O)N=C(O)CN=C([C@@H](N=C([C@@H](OC1=O)Cc1ccccc1)O)C)O)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL224345
PubChem CID:	16216414
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000264] Organic acids and derivatives [CHEMONTID:0001813] Peptidomimetics [CHEMONTID:0001961] Depsipeptides [CHEMONTID:0001994] Cyclic depsipeptides

*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
NPO32982	paecilomyces cinnamomeus	Species	n.a.	Eukaryota	n.a.	n.a.	n.a.	PMID[17269825]
NPO32716	conoideocrella tenuis bcc 18627	Species	Clavicipitaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21473608]

☑ 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	4

Activity Type	# Activity
Cell Line	1
Organism	2
Others	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT91	Cell Line	KB	Homo sapiens	IC50	=	5900.0	nM	PMID[484764]
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	IC50	=	4900.0	nM	PMID[484764]
NPT27	Others	Unspecified		IC50	=	6600.0	nM	PMID[484764]
NPT485	Organism	Plasmodium falciparum (isolate K1 / Thailand)	Plasmodium falciparum K1	IC50	=	4900.0	nM	PMID[484765]

☑ 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 NPC56635 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	178
0.1-0.2	904
0.2-0.3	3772
0.3-0.4	12438
0.4-0.5	5494
0.5-0.6	10992
0.6-0.7	8465
0.7-0.8	424
0.8-0.85	15
0.85-0.9	11
0.9-0.95	3
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
0.869	High Similarity	NPC6570
0.8611	High Similarity	NPC470392
0.8609	High Similarity	NPC132771
0.8483	Intermediate Similarity	NPC244866
0.8414	Intermediate Similarity	NPC45191
0.8344	Intermediate Similarity	NPC207675
0.8344	Intermediate Similarity	NPC212699
0.8247	Intermediate Similarity	NPC245974
0.8235	Intermediate Similarity	NPC247298
0.8221	Intermediate Similarity	NPC196091
0.8204	Intermediate Similarity	NPC32064
0.814	Intermediate Similarity	NPC64140
0.814	Intermediate Similarity	NPC174122
0.8118	Intermediate Similarity	NPC315542
0.8092	Intermediate Similarity	NPC473407
0.8092	Intermediate Similarity	NPC91953
0.8092	Intermediate Similarity	NPC473378
0.8081	Intermediate Similarity	NPC234069
0.8072	Intermediate Similarity	NPC164608
0.807	Intermediate Similarity	NPC276120
0.8026	Intermediate Similarity	NPC197921
0.8012	Intermediate Similarity	NPC138083
0.7974	Intermediate Similarity	NPC212850
0.7974	Intermediate Similarity	NPC83289
0.7974	Intermediate Similarity	NPC189724
0.7974	Intermediate Similarity	NPC469360
0.7959	Intermediate Similarity	NPC296712
0.7949	Intermediate Similarity	NPC313414
0.7939	Intermediate Similarity	NPC186617
0.7919	Intermediate Similarity	NPC326966
0.7905	Intermediate Similarity	NPC325651
0.7892	Intermediate Similarity	NPC471568
0.7892	Intermediate Similarity	NPC473693
0.7877	Intermediate Similarity	NPC4974
0.7867	Intermediate Similarity	NPC471953
0.7857	Intermediate Similarity	NPC26108
0.7829	Intermediate Similarity	NPC29531
0.7821	Intermediate Similarity	NPC50548
0.7808	Intermediate Similarity	NPC476260
0.7808	Intermediate Similarity	NPC476241
0.78	Intermediate Similarity	NPC275538
0.7784	Intermediate Similarity	NPC269383
0.7784	Intermediate Similarity	NPC151030
0.7778	Intermediate Similarity	NPC305700
0.7778	Intermediate Similarity	NPC140915
0.7778	Intermediate Similarity	NPC197741
0.7778	Intermediate Similarity	NPC187028
0.7778	Intermediate Similarity	NPC10221
0.7778	Intermediate Similarity	NPC18249
0.7771	Intermediate Similarity	NPC473502
0.7765	Intermediate Similarity	NPC144314
0.7758	Intermediate Similarity	NPC472923
0.7755	Intermediate Similarity	NPC476179
0.7755	Intermediate Similarity	NPC476125
0.7751	Intermediate Similarity	NPC155506
0.7751	Intermediate Similarity	NPC473354
0.7751	Intermediate Similarity	NPC159767
0.775	Intermediate Similarity	NPC182119
0.7746	Intermediate Similarity	NPC294951
0.7738	Intermediate Similarity	NPC89831
0.7736	Intermediate Similarity	NPC115144
0.7736	Intermediate Similarity	NPC277857
0.7722	Intermediate Similarity	NPC5462
0.7719	Intermediate Similarity	NPC45037
0.7711	Intermediate Similarity	NPC50380
0.7711	Intermediate Similarity	NPC254700
0.7711	Intermediate Similarity	NPC179250
0.7709	Intermediate Similarity	NPC149962
0.7708	Intermediate Similarity	NPC319950
0.7707	Intermediate Similarity	NPC178466
0.7707	Intermediate Similarity	NPC63628
0.7692	Intermediate Similarity	NPC248670
0.7692	Intermediate Similarity	NPC273755
0.7688	Intermediate Similarity	NPC471526
0.7677	Intermediate Similarity	NPC318984
0.7677	Intermediate Similarity	NPC259800
0.7677	Intermediate Similarity	NPC241086
0.7677	Intermediate Similarity	NPC317741
0.7677	Intermediate Similarity	NPC282087
0.7677	Intermediate Similarity	NPC328137
0.7677	Intermediate Similarity	NPC318028
0.7655	Intermediate Similarity	NPC476183
0.7655	Intermediate Similarity	NPC263835
0.7651	Intermediate Similarity	NPC210950
0.7651	Intermediate Similarity	NPC63931
0.7651	Intermediate Similarity	NPC199738
0.7643	Intermediate Similarity	NPC222039
0.7643	Intermediate Similarity	NPC100478
0.7633	Intermediate Similarity	NPC230611
0.7622	Intermediate Similarity	NPC287757
0.7622	Intermediate Similarity	NPC319320
0.7603	Intermediate Similarity	NPC476184
0.7603	Intermediate Similarity	NPC476281
0.7602	Intermediate Similarity	NPC50016
0.7597	Intermediate Similarity	NPC6913
0.7588	Intermediate Similarity	NPC137627
0.7588	Intermediate Similarity	NPC306804
0.7588	Intermediate Similarity	NPC49315
0.7582	Intermediate Similarity	NPC123859
0.7578	Intermediate Similarity	NPC233702
0.7578	Intermediate Similarity	NPC471032
0.7578	Intermediate Similarity	NPC470935
0.7572	Intermediate Similarity	NPC263507
0.7572	Intermediate Similarity	NPC271958
0.7572	Intermediate Similarity	NPC134413
0.7572	Intermediate Similarity	NPC45112
0.7568	Intermediate Similarity	NPC211218
0.7566	Intermediate Similarity	NPC114102
0.7564	Intermediate Similarity	NPC299583
0.7564	Intermediate Similarity	NPC197239
0.7564	Intermediate Similarity	NPC326860
0.756	Intermediate Similarity	NPC107938
0.756	Intermediate Similarity	NPC294516
0.7556	Intermediate Similarity	NPC471563
0.7551	Intermediate Similarity	NPC142577
0.7551	Intermediate Similarity	NPC27581
0.7551	Intermediate Similarity	NPC474862
0.755	Intermediate Similarity	NPC478147
0.7544	Intermediate Similarity	NPC279871
0.7544	Intermediate Similarity	NPC473402
0.7544	Intermediate Similarity	NPC471165
0.7543	Intermediate Similarity	NPC471050
0.7543	Intermediate Similarity	NPC471049
0.7543	Intermediate Similarity	NPC471048
0.7541	Intermediate Similarity	NPC242728
0.7533	Intermediate Similarity	NPC476353
0.7531	Intermediate Similarity	NPC114659
0.7531	Intermediate Similarity	NPC139699
0.7529	Intermediate Similarity	NPC476321
0.7528	Intermediate Similarity	NPC473305
0.7528	Intermediate Similarity	NPC163961
0.7517	Intermediate Similarity	NPC95733
0.7517	Intermediate Similarity	NPC62101
0.7517	Intermediate Similarity	NPC237420
0.7516	Intermediate Similarity	NPC274732
0.7514	Intermediate Similarity	NPC475421
0.75	Intermediate Similarity	NPC241354
0.75	Intermediate Similarity	NPC17760
0.75	Intermediate Similarity	NPC204848
0.75	Intermediate Similarity	NPC41473
0.75	Intermediate Similarity	NPC476278
0.75	Intermediate Similarity	NPC160607
0.75	Intermediate Similarity	NPC312770
0.75	Intermediate Similarity	NPC14600
0.7484	Intermediate Similarity	NPC81026
0.7471	Intermediate Similarity	NPC90984
0.7471	Intermediate Similarity	NPC40234
0.7469	Intermediate Similarity	NPC153644
0.7468	Intermediate Similarity	NPC66518
0.7467	Intermediate Similarity	NPC29477
0.7466	Intermediate Similarity	NPC43275
0.7442	Intermediate Similarity	NPC476227
0.7442	Intermediate Similarity	NPC227778
0.7442	Intermediate Similarity	NPC158277
0.744	Intermediate Similarity	NPC223207
0.744	Intermediate Similarity	NPC158900
0.7439	Intermediate Similarity	NPC127402
0.7432	Intermediate Similarity	NPC160493
0.7431	Intermediate Similarity	NPC51345
0.7421	Intermediate Similarity	NPC266741
0.7416	Intermediate Similarity	NPC94862
0.7414	Intermediate Similarity	NPC269750
0.7414	Intermediate Similarity	NPC194671
0.7403	Intermediate Similarity	NPC214869
0.7396	Intermediate Similarity	NPC304074
0.7396	Intermediate Similarity	NPC471771
0.7396	Intermediate Similarity	NPC290755
0.7391	Intermediate Similarity	NPC9373
0.7391	Intermediate Similarity	NPC160378
0.7389	Intermediate Similarity	NPC471201
0.7386	Intermediate Similarity	NPC470112
0.7386	Intermediate Similarity	NPC167763
0.7386	Intermediate Similarity	NPC35961
0.7386	Intermediate Similarity	NPC86678
0.7386	Intermediate Similarity	NPC195749
0.7386	Intermediate Similarity	NPC470903
0.7386	Intermediate Similarity	NPC52029
0.7378	Intermediate Similarity	NPC478189
0.7368	Intermediate Similarity	NPC251571
0.7366	Intermediate Similarity	NPC311357
0.7365	Intermediate Similarity	NPC83279
0.7355	Intermediate Similarity	NPC169766
0.7329	Intermediate Similarity	NPC311737
0.7329	Intermediate Similarity	NPC16188
0.7329	Intermediate Similarity	NPC169328
0.7329	Intermediate Similarity	NPC38458
0.732	Intermediate Similarity	NPC155838
0.7312	Intermediate Similarity	NPC106183
0.731	Intermediate Similarity	NPC317254
0.7308	Intermediate Similarity	NPC475468
0.7305	Intermediate Similarity	NPC107602
0.7303	Intermediate Similarity	NPC299806
0.7301	Intermediate Similarity	NPC324081
0.7297	Intermediate Similarity	NPC190663
0.7293	Intermediate Similarity	NPC477526
0.729	Intermediate Similarity	NPC307123
0.729	Intermediate Similarity	NPC97870
0.729	Intermediate Similarity	NPC247018
0.7288	Intermediate Similarity	NPC469831
0.7285	Intermediate Similarity	NPC47667

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 NPC56635 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	130
0.1-0.2	480
0.2-0.3	976
0.3-0.4	1969
0.4-0.5	2389
0.5-0.6	2052
0.6-0.7	1006
0.7-0.8	144
0.8-0.85	2
0.85-0.9	2
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8776	High Similarity	NPD7596	Clinical (unspecified phase)
0.8447	Intermediate Similarity	NPD7608	Discontinued
0.8125	Intermediate Similarity	NPD7972	Discontinued
0.8089	Intermediate Similarity	NPD7131	Phase 3
0.8025	Intermediate Similarity	NPD6390	Discontinued
0.795	Intermediate Similarity	NPD8019	Approved
0.7871	Intermediate Similarity	NPD2976	Clinical (unspecified phase)
0.7826	Intermediate Similarity	NPD6502	Phase 2
0.78	Intermediate Similarity	NPD6798	Discontinued
0.7792	Intermediate Similarity	NPD7450	Phase 2
0.7748	Intermediate Similarity	NPD6233	Phase 2
0.7748	Intermediate Similarity	NPD7477	Discontinued
0.7748	Intermediate Similarity	NPD5729	Clinical (unspecified phase)
0.7736	Intermediate Similarity	NPD3536	Discontinued
0.7697	Intermediate Similarity	NPD5837	Clinical (unspecified phase)
0.7677	Intermediate Similarity	NPD1538	Phase 1
0.7677	Intermediate Similarity	NPD2239	Approved
0.7677	Intermediate Similarity	NPD2240	Approved
0.7677	Intermediate Similarity	NPD1519	Approved
0.7677	Intermediate Similarity	NPD1537	Approved
0.7632	Intermediate Similarity	NPD5745	Approved
0.7628	Intermediate Similarity	NPD7978	Discontinued
0.7616	Intermediate Similarity	NPD3136	Phase 2
0.7578	Intermediate Similarity	NPD4186	Clinical (unspecified phase)
0.7572	Intermediate Similarity	NPD7959	Clinical (unspecified phase)
0.7568	Intermediate Similarity	NPD6582	Phase 2
0.7568	Intermediate Similarity	NPD6583	Phase 3
0.7564	Intermediate Similarity	NPD1523	Approved
0.7564	Intermediate Similarity	NPD1522	Approved
0.7561	Intermediate Similarity	NPD6677	Suspended
0.756	Intermediate Similarity	NPD6746	Phase 2
0.7548	Intermediate Similarity	NPD1536	Approved
0.7546	Intermediate Similarity	NPD3455	Phase 2
0.7545	Intermediate Similarity	NPD8070	Approved
0.7529	Intermediate Similarity	NPD8014	Clinical (unspecified phase)
0.75	Intermediate Similarity	NPD6867	Clinical (unspecified phase)
0.75	Intermediate Similarity	NPD6866	Clinical (unspecified phase)
0.75	Intermediate Similarity	NPD5746	Approved
0.7455	Intermediate Similarity	NPD7615	Clinical (unspecified phase)
0.7451	Intermediate Similarity	NPD1048	Approved
0.745	Intermediate Similarity	NPD3676	Clinical (unspecified phase)
0.744	Intermediate Similarity	NPD8031	Discontinued
0.7436	Intermediate Similarity	NPD1520	Approved
0.7436	Intermediate Similarity	NPD1521	Approved
0.7434	Intermediate Similarity	NPD2614	Approved
0.7419	Intermediate Similarity	NPD6355	Discontinued
0.7417	Intermediate Similarity	NPD6584	Phase 3
0.7417	Intermediate Similarity	NPD7451	Discontinued
0.7412	Intermediate Similarity	NPD7484	Phase 3
0.7412	Intermediate Similarity	NPD7485	Phase 3
0.741	Intermediate Similarity	NPD5356	Approved
0.741	Intermediate Similarity	NPD5355	Approved
0.7407	Intermediate Similarity	NPD5348	Clinical (unspecified phase)
0.7405	Intermediate Similarity	NPD5865	Clinical (unspecified phase)
0.7403	Intermediate Similarity	NPD4062	Phase 3
0.74	Intermediate Similarity	NPD196	Phase 1
0.7383	Intermediate Similarity	NPD5108	Clinical (unspecified phase)
0.7375	Intermediate Similarity	NPD3400	Discontinued
0.7372	Intermediate Similarity	NPD3052	Approved
0.7372	Intermediate Similarity	NPD3054	Approved
0.7371	Intermediate Similarity	NPD6211	Clinical (unspecified phase)
0.7371	Intermediate Similarity	NPD3823	Discontinued
0.7368	Intermediate Similarity	NPD7315	Approved
0.7356	Intermediate Similarity	NPD3965	Phase 1
0.7349	Intermediate Similarity	NPD2541	Clinical (unspecified phase)
0.7349	Intermediate Similarity	NPD3274	Phase 2
0.7349	Intermediate Similarity	NPD6072	Discontinued
0.7342	Intermediate Similarity	NPD6032	Approved
0.7325	Intermediate Similarity	NPD5688	Approved
0.7325	Intermediate Similarity	NPD5689	Approved
0.7314	Intermediate Similarity	NPD5557	Phase 1
0.7305	Intermediate Similarity	NPD4433	Discontinued
0.7305	Intermediate Similarity	NPD7495	Discontinued
0.7305	Intermediate Similarity	NPD7945	Clinical (unspecified phase)
0.7303	Intermediate Similarity	NPD6556	Clinical (unspecified phase)
0.7299	Intermediate Similarity	NPD3909	Discontinued
0.7297	Intermediate Similarity	NPD7565	Approved
0.7296	Intermediate Similarity	NPD3656	Approved
0.729	Intermediate Similarity	NPD1423	Approved
0.7273	Intermediate Similarity	NPD4003	Phase 3
0.7267	Intermediate Similarity	NPD6331	Phase 2
0.7267	Intermediate Similarity	NPD6658	Clinical (unspecified phase)
0.7262	Intermediate Similarity	NPD5563	Clinical (unspecified phase)
0.7262	Intermediate Similarity	NPD3465	Clinical (unspecified phase)
0.7255	Intermediate Similarity	NPD4993	Discontinued
0.725	Intermediate Similarity	NPD2897	Discontinued
0.725	Intermediate Similarity	NPD7153	Discontinued
0.7239	Intermediate Similarity	NPD6682	Clinical (unspecified phase)
0.7235	Intermediate Similarity	NPD7975	Clinical (unspecified phase)
0.7233	Intermediate Similarity	NPD4477	Approved
0.7233	Intermediate Similarity	NPD4476	Approved
0.7232	Intermediate Similarity	NPD7039	Approved
0.7232	Intermediate Similarity	NPD7038	Approved
0.723	Intermediate Similarity	NPD6830	Clinical (unspecified phase)
0.7226	Intermediate Similarity	NPD3374	Clinical (unspecified phase)
0.7226	Intermediate Similarity	NPD3056	Clinical (unspecified phase)
0.7219	Intermediate Similarity	NPD3685	Discontinued
0.7212	Intermediate Similarity	NPD7427	Discontinued
0.7204	Intermediate Similarity	NPD7811	Phase 3
0.7204	Intermediate Similarity	NPD7810	Phase 3
0.7202	Intermediate Similarity	NPD4018	Clinical (unspecified phase)
0.7197	Intermediate Similarity	NPD4622	Approved
0.7197	Intermediate Similarity	NPD555	Phase 2
0.7197	Intermediate Similarity	NPD4618	Approved
0.7195	Intermediate Similarity	NPD4123	Phase 3
0.7195	Intermediate Similarity	NPD3985	Discontinued
0.7195	Intermediate Similarity	NPD7446	Clinical (unspecified phase)
0.7195	Intermediate Similarity	NPD4739	Approved
0.7184	Intermediate Similarity	NPD7784	Clinical (unspecified phase)
0.7184	Intermediate Similarity	NPD5822	Clinical (unspecified phase)
0.7178	Intermediate Similarity	NPD6666	Approved
0.7178	Intermediate Similarity	NPD6667	Approved
0.7176	Intermediate Similarity	NPD7773	Phase 2
0.7167	Intermediate Similarity	NPD6967	Phase 2
0.7162	Intermediate Similarity	NPD6581	Approved
0.7162	Intermediate Similarity	NPD6580	Approved
0.7162	Intermediate Similarity	NPD1894	Discontinued
0.7161	Intermediate Similarity	NPD7095	Approved
0.7161	Intermediate Similarity	NPD5163	Phase 2
0.716	Intermediate Similarity	NPD5773	Approved
0.716	Intermediate Similarity	NPD5772	Approved
0.7152	Intermediate Similarity	NPD52	Approved
0.7152	Intermediate Similarity	NPD7526	Approved
0.7152	Intermediate Similarity	NPD7527	Clinical (unspecified phase)
0.7151	Intermediate Similarity	NPD4666	Phase 3
0.7135	Intermediate Similarity	NPD8005	Clinical (unspecified phase)
0.7133	Intermediate Similarity	NPD3847	Discontinued
0.7126	Intermediate Similarity	NPD8158	Clinical (unspecified phase)
0.7118	Intermediate Similarity	NPD7318	Phase 3
0.7115	Intermediate Similarity	NPD6859	Clinical (unspecified phase)
0.7108	Intermediate Similarity	NPD7523	Phase 3
0.7107	Intermediate Similarity	NPD7097	Phase 1
0.7099	Intermediate Similarity	NPD2459	Approved
0.7099	Intermediate Similarity	NPD2458	Approved
0.7099	Intermediate Similarity	NPD2460	Phase 3
0.7095	Intermediate Similarity	NPD7132	Clinical (unspecified phase)
0.7093	Intermediate Similarity	NPD5709	Phase 3
0.7093	Intermediate Similarity	NPD6315	Phase 2
0.7086	Intermediate Similarity	NPD1535	Discovery
0.7081	Intermediate Similarity	NPD6312	Discontinued
0.707	Intermediate Similarity	NPD259	Phase 1
0.707	Intermediate Similarity	NPD2674	Phase 3
0.7056	Intermediate Similarity	NPD7546	Discontinued
0.7055	Intermediate Similarity	NPD4110	Phase 3
0.7055	Intermediate Similarity	NPD4109	Clinical (unspecified phase)
0.7055	Intermediate Similarity	NPD4628	Phase 3
0.7048	Intermediate Similarity	NPD5261	Clinical (unspecified phase)
0.7041	Intermediate Similarity	NPD3778	Approved
0.7041	Intermediate Similarity	NPD6386	Approved
0.7041	Intermediate Similarity	NPD6385	Approved
0.7039	Intermediate Similarity	NPD1481	Phase 2
0.7035	Intermediate Similarity	NPD6971	Discontinued
0.703	Intermediate Similarity	NPD7212	Phase 2
0.703	Intermediate Similarity	NPD7213	Phase 3
0.7027	Intermediate Similarity	NPD9568	Approved
0.7025	Intermediate Similarity	NPD826	Approved
0.7025	Intermediate Similarity	NPD825	Approved
0.7024	Intermediate Similarity	NPD5811	Approved
0.7019	Intermediate Similarity	NPD2161	Phase 2
0.7019	Intermediate Similarity	NPD3175	Clinical (unspecified phase)
0.7017	Intermediate Similarity	NPD6853	Approved
0.7017	Intermediate Similarity	NPD6851	Approved
0.7006	Intermediate Similarity	NPD6620	Discovery
0.7	Intermediate Similarity	NPD7577	Discontinued
0.7	Intermediate Similarity	NPD7317	Phase 3
0.6994	Remote Similarity	NPD8245	Clinical (unspecified phase)
0.6994	Remote Similarity	NPD6862	Phase 2
0.6994	Remote Similarity	NPD7421	Clinical (unspecified phase)
0.6988	Remote Similarity	NPD7447	Phase 1
0.6986	Remote Similarity	NPD821	Approved
0.6986	Remote Similarity	NPD7843	Approved
0.6986	Remote Similarity	NPD5535	Approved
0.6983	Remote Similarity	NPD7007	Discovery
0.6982	Remote Similarity	NPD4675	Approved
0.6982	Remote Similarity	NPD4678	Approved
0.6973	Remote Similarity	NPD3819	Phase 2
0.6964	Remote Similarity	NPD3686	Approved
0.6964	Remote Similarity	NPD3687	Approved
0.6962	Remote Similarity	NPD7265	Discontinued
0.6959	Remote Similarity	NPD7046	Clinical (unspecified phase)
0.6959	Remote Similarity	NPD8455	Phase 2
0.6957	Remote Similarity	NPD7861	Discontinued
0.6948	Remote Similarity	NPD7258	Clinical (unspecified phase)
0.6943	Remote Similarity	NPD4738	Phase 2
0.6941	Remote Similarity	NPD7438	Suspended
0.6941	Remote Similarity	NPD7118	Clinical (unspecified phase)
0.6937	Remote Similarity	NPD4579	Clinical (unspecified phase)
0.6935	Remote Similarity	NPD4466	Phase 1
0.6933	Remote Similarity	NPD1759	Phase 1
0.6933	Remote Similarity	NPD3655	Clinical (unspecified phase)
0.6933	Remote Similarity	NPD4534	Discontinued
0.6933	Remote Similarity	NPD2030	Discontinued
0.6918	Remote Similarity	NPD4060	Phase 1
0.6918	Remote Similarity	NPD6346	Approved
0.6913	Remote Similarity	NPD3596	Phase 2
0.691	Remote Similarity	NPD7493	Clinical (unspecified phase)
0.6909	Remote Similarity	NPD5241	Discontinued
0.6909	Remote Similarity	NPD3692	Discontinued
0.6903	Remote Similarity	NPD1820	Approved
0.6903	Remote Similarity	NPD1817	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