NPASS Compound

Structure

NPC6570 OpenBabel07101718222D 43 44 0 0 1 0 0 0 0 0999 V2000 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 -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 6.1953 2.4397 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 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 -0.5240 -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 6.1953 -2.4397 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 2.3794 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 -1.3900 0.9397 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.1953 1.4397 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 8.7934 -0.9397 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.3293 -1.9397 0.0000 C 0 0 1 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 1.8508 -3.2057 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 5.3293 0.9397 0.0000 C 0 0 1 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 5.6713 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 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 0.9848 -2.7057 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 4.6865 1.7057 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 1.5088 -4.1454 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 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 6.6561 0.1736 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 -0.0000 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 16 1 0 0 0 0 2 16 1 0 0 0 0 3 17 1 0 0 0 0 4 17 1 0 0 0 0 5 18 1 0 0 0 0 6 18 1 0 0 0 0 7 9 1 0 0 0 0 7 19 2 0 0 0 0 8 10 2 0 0 0 0 8 19 1 0 0 0 0 9 20 2 0 0 0 0 10 20 1 0 0 0 0 11 16 1 0 0 0 0 12 17 1 0 0 0 0 13 19 1 0 0 0 0 14 24 1 0 0 0 0 14 31 1 0 0 0 0 15 25 1 0 0 0 0 15 32 1 0 0 0 0 20 36 1 0 0 0 0 21 13 1 1 0 0 0 21 27 1 0 0 0 0 21 34 1 0 0 0 0 22 11 1 6 0 0 0 22 30 1 0 0 0 0 22 33 1 0 0 0 0 23 12 1 1 0 0 0 23 28 1 0 0 0 0 23 43 1 0 0 0 0 24 33 2 3 0 0 0 24 37 1 0 0 0 0 25 35 2 3 0 0 0 25 38 1 0 0 0 0 26 18 1 1 0 0 0 26 29 1 0 0 0 0 26 35 1 0 0 0 0 27 31 2 3 0 0 0 27 39 1 0 0 0 0 28 32 2 3 0 0 0 28 40 1 0 0 0 0 29 34 2 3 0 0 0 29 41 1 0 0 0 0 30 42 2 0 0 0 0 30 43 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	603.33
Volume:	611.901
LogP:	2.463
LogD:	3.104
LogS:	-4.165
# Rotatable Bonds:	7
TPSA:	192.03
# H-Bond Aceptor:	13
# H-Bond Donor:	6
# Rings:	2
# Heavy Atoms:	13

MedChem Properties

QED Drug-Likeness Score:	0.24
Synthetic Accessibility Score:	4.782
Fsp3:	0.6
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:	-5.979
MDCK Permeability:	7.530939910793677e-06
Pgp-inhibitor:	0.571
Pgp-substrate:	0.993
Human Intestinal Absorption (HIA):	0.01
20% Bioavailability (F20%):	0.075
30% Bioavailability (F30%):	0.914

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.095
Plasma Protein Binding (PPB):	55.878726959228516%
Volume Distribution (VD):	0.276
Pgp-substrate:	28.599506378173828%

ADMET: Metabolism

CYP1A2-inhibitor:	0.003
CYP1A2-substrate:	0.016
CYP2C19-inhibitor:	0.173
CYP2C19-substrate:	0.047
CYP2C9-inhibitor:	0.286
CYP2C9-substrate:	0.072
CYP2D6-inhibitor:	0.001
CYP2D6-substrate:	0.077
CYP3A4-inhibitor:	0.678
CYP3A4-substrate:	0.092

ADMET: Excretion

Clearance (CL):	6.519
Half-life (T1/2):	0.773

ADMET: Toxicity

hERG Blockers:	0.043
Human Hepatotoxicity (H-HT):	0.72
Drug-inuced Liver Injury (DILI):	0.045
AMES Toxicity:	0.005
Rat Oral Acute Toxicity:	0.056
Maximum Recommended Daily Dose:	0.208
Skin Sensitization:	0.13
Carcinogencity:	0.027
Eye Corrosion:	0.003
Eye Irritation:	0.005
Respiratory Toxicity:	0.04

Download Data

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

Natural Product: NPC6570

Natural Product ID:	NPC6570
*Common Name:**	Cyclo-(D-Leu-Gly-L-Tyr-L-Val-Gly-S-O-Leu)
IUPAC Name:	(3R,9S,12S,18S)-9-[(4-hydroxyphenyl)methyl]-3,18-bis(2-methylpropyl)-12-propan-2-yl-1-oxa-4,7,10,13,16-pentazacyclooctadecane-2,5,8,11,14,17-hexone
Synonyms:
Standard InCHIKey:	YHTLEEMONFFJCU-LNEBKTTKSA-N
Standard InCHI:	InChI=1S/C30H45N5O8/c1-16(2)11-22-30(42)43-23(12-17(3)4)28(40)32-15-25(38)35-26(18(5)6)29(41)34-21(27(39)31-14-24(37)33-22)13-19-7-9-20(36)10-8-19/h7-10,16-18,21-23,26,36H,11-15H2,1-6H3,(H,31,39)(H,32,40)(H,33,37)(H,34,41)(H,35,38)/t21-,22+,23-,26-/m0/s1
SMILES:	CC(C)C[C@@H]1C(=O)O[C@@H](CC(C)C)C(=NCC(=N[C@@H](C(C)C)C(=N[C@@H](Cc2ccc(cc2)O)C(=NCC(=N1)O)O)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL404847
PubChem CID:	24178774
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
NPO14254	Kandelia candel	Species	Rhizophoraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[17944538]
NPO14254	Kandelia candel	Species	Rhizophoraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[22823026]
NPO14254	Kandelia candel	Species	Rhizophoraceae	Eukaryota	leaves and stems	Ha Long, Quang Ninh province, Vietnam	2014-Jul	PMID[25769817]
NPO14254	Kandelia candel	Species	Rhizophoraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[29792702]
NPO14254	Kandelia candel	Species	Rhizophoraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO14254	Kandelia candel	Species	Rhizophoraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO14254	Kandelia candel	Species	Rhizophoraceae	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
NPT83	Cell Line	MCF7	Homo sapiens	IC50	=	100.0	ug.mL-1	PMID[514378]

☑ 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 NPC6570 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	134
0.1-0.2	691
0.2-0.3	3409
0.3-0.4	12054
0.4-0.5	8969
0.5-0.6	14334
0.6-0.7	2640
0.7-0.8	399
0.8-0.85	45
0.85-0.9	15
0.9-0.95	5
0.95-1	2

Similarity Score	Similarity Level	Natural Product ID
0.9111	High Similarity	NPC91953
0.9037	High Similarity	NPC197921
0.8971	High Similarity	NPC469360
0.8855	High Similarity	NPC296712
0.869	High Similarity	NPC56635
0.8682	High Similarity	NPC474862
0.8657	High Similarity	NPC45191
0.8657	High Similarity	NPC326966
0.8516	High Similarity	NPC237420
0.8511	High Similarity	NPC81026
0.845	Intermediate Similarity	NPC319950
0.844	Intermediate Similarity	NPC266741
0.8425	Intermediate Similarity	NPC317254
0.8409	Intermediate Similarity	NPC476260
0.8409	Intermediate Similarity	NPC476241
0.8385	Intermediate Similarity	NPC476183
0.837	Intermediate Similarity	NPC478147
0.8346	Intermediate Similarity	NPC476179
0.8346	Intermediate Similarity	NPC476125
0.8333	Intermediate Similarity	NPC132771
0.8321	Intermediate Similarity	NPC244866
0.8321	Intermediate Similarity	NPC476184
0.8321	Intermediate Similarity	NPC476281
0.8258	Intermediate Similarity	NPC27581
0.8258	Intermediate Similarity	NPC142577
0.8235	Intermediate Similarity	NPC325651
0.8231	Intermediate Similarity	NPC39431
0.8222	Intermediate Similarity	NPC476353
0.8195	Intermediate Similarity	NPC476278
0.8188	Intermediate Similarity	NPC470392
0.8168	Intermediate Similarity	NPC283760
0.8141	Intermediate Similarity	NPC473354
0.8141	Intermediate Similarity	NPC26108
0.8116	Intermediate Similarity	NPC275538
0.8077	Intermediate Similarity	NPC248670
0.8077	Intermediate Similarity	NPC273755
0.8067	Intermediate Similarity	NPC207675
0.8067	Intermediate Similarity	NPC212699
0.8065	Intermediate Similarity	NPC196091
0.8028	Intermediate Similarity	NPC471201
0.8025	Intermediate Similarity	NPC471165
0.8015	Intermediate Similarity	NPC169328
0.8014	Intermediate Similarity	NPC64205
0.8	Intermediate Similarity	NPC186617
0.7975	Intermediate Similarity	NPC50016
0.797	Intermediate Similarity	NPC190663
0.7955	Intermediate Similarity	NPC310467
0.7949	Intermediate Similarity	NPC473693
0.7949	Intermediate Similarity	NPC471568
0.7935	Intermediate Similarity	NPC294516
0.7935	Intermediate Similarity	NPC107938
0.7923	Intermediate Similarity	NPC118202
0.7922	Intermediate Similarity	NPC63931
0.7902	Intermediate Similarity	NPC322526
0.7898	Intermediate Similarity	NPC89831
0.7891	Intermediate Similarity	NPC474149
0.7888	Intermediate Similarity	NPC476321
0.7887	Intermediate Similarity	NPC6913
0.7875	Intermediate Similarity	NPC45037
0.7852	Intermediate Similarity	NPC476744
0.7852	Intermediate Similarity	NPC160493
0.784	Intermediate Similarity	NPC471526
0.7834	Intermediate Similarity	NPC40234
0.7834	Intermediate Similarity	NPC475123
0.7834	Intermediate Similarity	NPC475204
0.7834	Intermediate Similarity	NPC46009
0.7832	Intermediate Similarity	NPC473055
0.7832	Intermediate Similarity	NPC473052
0.7821	Intermediate Similarity	NPC209463
0.7812	Intermediate Similarity	NPC258056
0.781	Intermediate Similarity	NPC4974
0.7806	Intermediate Similarity	NPC472923
0.7801	Intermediate Similarity	NPC328070
0.7793	Intermediate Similarity	NPC168861
0.7785	Intermediate Similarity	NPC230611
0.7785	Intermediate Similarity	NPC476743
0.7778	Intermediate Similarity	NPC48202
0.7769	Intermediate Similarity	NPC273814
0.7762	Intermediate Similarity	NPC127741
0.7744	Intermediate Similarity	NPC38458
0.7744	Intermediate Similarity	NPC311737
0.7736	Intermediate Similarity	NPC137627
0.7736	Intermediate Similarity	NPC306804
0.7727	Intermediate Similarity	NPC476194
0.7717	Intermediate Similarity	NPC231705
0.7704	Intermediate Similarity	NPC80150
0.7704	Intermediate Similarity	NPC477061
0.7704	Intermediate Similarity	NPC45777
0.7697	Intermediate Similarity	NPC476741
0.7697	Intermediate Similarity	NPC476268
0.7688	Intermediate Similarity	NPC279871
0.7688	Intermediate Similarity	NPC159767
0.7688	Intermediate Similarity	NPC473402
0.7688	Intermediate Similarity	NPC155506
0.7688	Intermediate Similarity	NPC476227
0.7687	Intermediate Similarity	NPC314992
0.7683	Intermediate Similarity	NPC471048
0.7683	Intermediate Similarity	NPC294951
0.7683	Intermediate Similarity	NPC471049
0.7683	Intermediate Similarity	NPC471050
0.7682	Intermediate Similarity	NPC262166
0.7676	Intermediate Similarity	NPC88667
0.7669	Intermediate Similarity	NPC188867
0.7669	Intermediate Similarity	NPC82963
0.7669	Intermediate Similarity	NPC106551
0.7669	Intermediate Similarity	NPC281686
0.7656	Intermediate Similarity	NPC142297
0.7639	Intermediate Similarity	NPC68865
0.7632	Intermediate Similarity	NPC476742
0.7597	Intermediate Similarity	NPC31274
0.7595	Intermediate Similarity	NPC473502
0.7584	Intermediate Similarity	NPC16188
0.7582	Intermediate Similarity	NPC473580
0.7578	Intermediate Similarity	NPC227778
0.7578	Intermediate Similarity	NPC158277
0.7576	Intermediate Similarity	NPC309808
0.7576	Intermediate Similarity	NPC1986
0.7576	Intermediate Similarity	NPC474544
0.7554	Intermediate Similarity	NPC47667
0.7551	Intermediate Similarity	NPC83289
0.7551	Intermediate Similarity	NPC189724
0.7551	Intermediate Similarity	NPC212850
0.755	Intermediate Similarity	NPC473491
0.7546	Intermediate Similarity	NPC269750
0.7546	Intermediate Similarity	NPC194671
0.7537	Intermediate Similarity	NPC2265
0.7532	Intermediate Similarity	NPC15506
0.7515	Intermediate Similarity	NPC473378
0.7515	Intermediate Similarity	NPC473407
0.75	Intermediate Similarity	NPC48525
0.75	Intermediate Similarity	NPC233702
0.75	Intermediate Similarity	NPC151030
0.75	Intermediate Similarity	NPC102959
0.75	Intermediate Similarity	NPC239697
0.75	Intermediate Similarity	NPC469243
0.75	Intermediate Similarity	NPC269383
0.7483	Intermediate Similarity	NPC476989
0.748	Intermediate Similarity	NPC178902
0.7467	Intermediate Similarity	NPC135121
0.7456	Intermediate Similarity	NPC60516
0.7456	Intermediate Similarity	NPC473305
0.7456	Intermediate Similarity	NPC163961
0.7455	Intermediate Similarity	NPC473404
0.7453	Intermediate Similarity	NPC83241
0.7452	Intermediate Similarity	NPC156348
0.7451	Intermediate Similarity	NPC261934
0.7451	Intermediate Similarity	NPC202198
0.7451	Intermediate Similarity	NPC5194
0.7451	Intermediate Similarity	NPC56685
0.745	Intermediate Similarity	NPC477217
0.745	Intermediate Similarity	NPC106183
0.745	Intermediate Similarity	NPC201244
0.7447	Intermediate Similarity	NPC210950
0.7447	Intermediate Similarity	NPC199738
0.7445	Intermediate Similarity	NPC478016
0.7445	Intermediate Similarity	NPC478014
0.7445	Intermediate Similarity	NPC478015
0.744	Intermediate Similarity	NPC94862
0.7431	Intermediate Similarity	NPC274732
0.7431	Intermediate Similarity	NPC471953
0.7425	Intermediate Similarity	NPC315542
0.7417	Intermediate Similarity	NPC313414
0.741	Intermediate Similarity	NPC469927
0.741	Intermediate Similarity	NPC35996
0.7394	Intermediate Similarity	NPC16031
0.7394	Intermediate Similarity	NPC161593
0.7394	Intermediate Similarity	NPC145888
0.7391	Intermediate Similarity	NPC56634
0.7389	Intermediate Similarity	NPC471203
0.7389	Intermediate Similarity	NPC475544
0.7372	Intermediate Similarity	NPC268572
0.7368	Intermediate Similarity	NPC245974
0.7368	Intermediate Similarity	NPC474584
0.7365	Intermediate Similarity	NPC168113
0.7362	Intermediate Similarity	NPC95412
0.7358	Intermediate Similarity	NPC223207
0.7355	Intermediate Similarity	NPC244509
0.7351	Intermediate Similarity	NPC247298
0.7333	Intermediate Similarity	NPC475421
0.7333	Intermediate Similarity	NPC37302
0.7329	Intermediate Similarity	NPC280022
0.7328	Intermediate Similarity	NPC96224
0.7328	Intermediate Similarity	NPC24101
0.7326	Intermediate Similarity	NPC302715
0.7326	Intermediate Similarity	NPC65714
0.7315	Intermediate Similarity	NPC197682
0.7315	Intermediate Similarity	NPC176226
0.7312	Intermediate Similarity	NPC290755
0.7312	Intermediate Similarity	NPC304074
0.7312	Intermediate Similarity	NPC61004
0.7312	Intermediate Similarity	NPC471771
0.731	Intermediate Similarity	NPC474753
0.7301	Intermediate Similarity	NPC49315
0.7299	Intermediate Similarity	NPC317784
0.7299	Intermediate Similarity	NPC142638
0.7297	Intermediate Similarity	NPC307357
0.7297	Intermediate Similarity	NPC46098
0.7297	Intermediate Similarity	NPC268841
0.7293	Intermediate Similarity	NPC227553
0.7293	Intermediate Similarity	NPC163674

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 NPC6570 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	108
0.1-0.2	382
0.2-0.3	928
0.3-0.4	2119
0.4-0.5	2802
0.5-0.6	2086
0.6-0.7	661
0.7-0.8	61
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
0.8872	High Similarity	NPD5729	Clinical (unspecified phase)
0.8722	High Similarity	NPD3136	Phase 2
0.8429	Intermediate Similarity	NPD7978	Discontinued
0.8028	Intermediate Similarity	NPD6867	Clinical (unspecified phase)
0.8028	Intermediate Similarity	NPD6866	Clinical (unspecified phase)
0.7973	Intermediate Similarity	NPD6390	Discontinued
0.7838	Intermediate Similarity	NPD6682	Clinical (unspecified phase)
0.7817	Intermediate Similarity	NPD555	Phase 2
0.78	Intermediate Similarity	NPD7523	Phase 3
0.7778	Intermediate Similarity	NPD8019	Approved
0.7727	Intermediate Similarity	NPD7972	Discontinued
0.7724	Intermediate Similarity	NPD7450	Phase 2
0.7722	Intermediate Similarity	NPD7608	Discontinued
0.7687	Intermediate Similarity	NPD2218	Phase 2
0.7687	Intermediate Similarity	NPD2217	Approved
0.7676	Intermediate Similarity	NPD259	Phase 1
0.7669	Intermediate Similarity	NPD9568	Approved
0.7662	Intermediate Similarity	NPD7495	Discontinued
0.766	Intermediate Similarity	NPD4738	Phase 2
0.7635	Intermediate Similarity	NPD3400	Discontinued
0.7622	Intermediate Similarity	NPD826	Approved
0.7622	Intermediate Similarity	NPD825	Approved
0.7619	Intermediate Similarity	NPD7596	Clinical (unspecified phase)
0.7609	Intermediate Similarity	NPD3676	Clinical (unspecified phase)
0.7571	Intermediate Similarity	NPD7451	Discontinued
0.7556	Intermediate Similarity	NPD1759	Phase 1
0.75	Intermediate Similarity	NPD4186	Clinical (unspecified phase)
0.7484	Intermediate Similarity	NPD7118	Clinical (unspecified phase)
0.7481	Intermediate Similarity	NPD1758	Phase 1
0.7468	Intermediate Similarity	NPD3455	Phase 2
0.7463	Intermediate Similarity	NPD256	Approved
0.7463	Intermediate Similarity	NPD255	Approved
0.7434	Intermediate Similarity	NPD5348	Clinical (unspecified phase)
0.7431	Intermediate Similarity	NPD5745	Approved
0.741	Intermediate Similarity	NPD5108	Clinical (unspecified phase)
0.7394	Intermediate Similarity	NPD9569	Approved
0.7379	Intermediate Similarity	NPD6346	Approved
0.7338	Intermediate Similarity	NPD7131	Phase 3
0.7312	Intermediate Similarity	NPD8303	Discontinued
0.7292	Intermediate Similarity	NPD5746	Approved
0.7289	Intermediate Similarity	NPD7959	Clinical (unspecified phase)
0.7248	Intermediate Similarity	NPD2240	Approved
0.7248	Intermediate Similarity	NPD9570	Approved
0.7248	Intermediate Similarity	NPD2239	Approved
0.7246	Intermediate Similarity	NPD8014	Clinical (unspecified phase)
0.7241	Intermediate Similarity	NPD1048	Approved
0.7208	Intermediate Similarity	NPD3536	Discontinued
0.7208	Intermediate Similarity	NPD4739	Approved
0.7203	Intermediate Similarity	NPD258	Approved
0.7203	Intermediate Similarity	NPD257	Approved
0.7183	Intermediate Similarity	NPD196	Phase 1
0.7172	Intermediate Similarity	NPD9537	Phase 1
0.7172	Intermediate Similarity	NPD9536	Phase 1
0.7113	Intermediate Similarity	NPD3685	Discontinued
0.7113	Intermediate Similarity	NPD4659	Approved
0.7105	Intermediate Similarity	NPD2976	Clinical (unspecified phase)
0.7101	Intermediate Similarity	NPD318	Approved
0.7101	Intermediate Similarity	NPD317	Approved
0.7092	Intermediate Similarity	NPD4806	Approved
0.7092	Intermediate Similarity	NPD4807	Approved
0.708	Intermediate Similarity	NPD1348	Approved
0.7075	Intermediate Similarity	NPD2674	Phase 3
0.7075	Intermediate Similarity	NPD1423	Approved
0.7063	Intermediate Similarity	NPD5563	Clinical (unspecified phase)
0.7051	Intermediate Similarity	NPD7527	Clinical (unspecified phase)
0.7051	Intermediate Similarity	NPD52	Approved
0.7051	Intermediate Similarity	NPD7526	Approved
0.7042	Intermediate Similarity	NPD2561	Approved
0.7042	Intermediate Similarity	NPD6624	Discontinued
0.7042	Intermediate Similarity	NPD2562	Approved
0.7039	Intermediate Similarity	NPD7153	Discontinued
0.7039	Intermediate Similarity	NPD6119	Clinical (unspecified phase)
0.7023	Intermediate Similarity	NPD9608	Approved
0.7023	Intermediate Similarity	NPD9610	Approved
0.7021	Intermediate Similarity	NPD3421	Phase 3
0.7015	Intermediate Similarity	NPD9380	Clinical (unspecified phase)
0.7014	Intermediate Similarity	NPD2159	Approved
0.7014	Intermediate Similarity	NPD2625	Approved
0.7014	Intermediate Similarity	NPD2626	Approved
0.7014	Intermediate Similarity	NPD2160	Approved
0.7014	Intermediate Similarity	NPD2627	Approved
0.7014	Intermediate Similarity	NPD2628	Approved
0.7012	Intermediate Similarity	NPD7484	Phase 3
0.7012	Intermediate Similarity	NPD7485	Phase 3
0.7007	Intermediate Similarity	NPD3144	Approved
0.7007	Intermediate Similarity	NPD3145	Approved
0.7	Intermediate Similarity	NPD6852	Discontinued
0.7	Intermediate Similarity	NPD5356	Approved
0.7	Intermediate Similarity	NPD5355	Approved
0.6986	Remote Similarity	NPD5202	Clinical (unspecified phase)
0.698	Remote Similarity	NPD274	Approved
0.698	Remote Similarity	NPD275	Approved
0.6978	Remote Similarity	NPD856	Approved
0.6978	Remote Similarity	NPD16	Approved
0.6974	Remote Similarity	NPD3656	Approved
0.697	Remote Similarity	NPD1040	Phase 2
0.6963	Remote Similarity	NPD3644	Approved
0.6963	Remote Similarity	NPD3643	Approved
0.6963	Remote Similarity	NPD3642	Approved
0.6943	Remote Similarity	NPD7303	Discontinued
0.6934	Remote Similarity	NPD2229	Approved
0.6934	Remote Similarity	NPD2234	Approved
0.6934	Remote Similarity	NPD2228	Approved
0.6933	Remote Similarity	NPD7975	Clinical (unspecified phase)
0.6928	Remote Similarity	NPD6681	Discovery
0.6918	Remote Similarity	NPD3663	Approved
0.6918	Remote Similarity	NPD3661	Approved
0.6918	Remote Similarity	NPD3662	Phase 3
0.6918	Remote Similarity	NPD3664	Approved
0.6908	Remote Similarity	NPD1538	Phase 1
0.6908	Remote Similarity	NPD1537	Approved
0.6908	Remote Similarity	NPD4173	Approved
0.6908	Remote Similarity	NPD4172	Approved
0.6908	Remote Similarity	NPD1519	Approved
0.6908	Remote Similarity	NPD2161	Phase 2
0.6906	Remote Similarity	NPD3123	Discovery
0.6901	Remote Similarity	NPD4135	Approved
0.6901	Remote Similarity	NPD4106	Approved
0.6901	Remote Similarity	NPD4136	Approved
0.6897	Remote Similarity	NPD4103	Phase 2
0.6897	Remote Similarity	NPD4104	Clinical (unspecified phase)
0.6892	Remote Similarity	NPD4621	Approved
0.6892	Remote Similarity	NPD4619	Approved
0.6887	Remote Similarity	NPD3554	Approved
0.6887	Remote Similarity	NPD3555	Approved
0.6887	Remote Similarity	NPD3552	Approved
0.6887	Remote Similarity	NPD3553	Approved
0.6884	Remote Similarity	NPD9614	Approved
0.6884	Remote Similarity	NPD9618	Approved
0.6879	Remote Similarity	NPD5981	Approved
0.6875	Remote Similarity	NPD6502	Phase 2
0.6875	Remote Similarity	NPD9622	Approved
0.6871	Remote Similarity	NPD2614	Approved
0.6871	Remote Similarity	NPD5201	Approved
0.6871	Remote Similarity	NPD4617	Approved
0.6871	Remote Similarity	NPD4620	Approved
0.6871	Remote Similarity	NPD5203	Approved
0.6867	Remote Similarity	NPD7315	Approved
0.6853	Remote Similarity	NPD4480	Approved
0.6852	Remote Similarity	NPD5772	Approved
0.6852	Remote Similarity	NPD5773	Approved
0.6846	Remote Similarity	NPD7477	Discontinued
0.6839	Remote Similarity	NPD7066	Clinical (unspecified phase)
0.6833	Remote Similarity	NPD7565	Approved
0.6832	Remote Similarity	NPD6677	Suspended
0.6832	Remote Similarity	NPD2541	Clinical (unspecified phase)
0.6832	Remote Similarity	NPD6072	Discontinued
0.6831	Remote Similarity	NPD5306	Approved
0.6831	Remote Similarity	NPD5305	Approved
0.6831	Remote Similarity	NPD5238	Clinical (unspecified phase)
0.6829	Remote Similarity	NPD2098	Approved
0.6824	Remote Similarity	NPD5557	Phase 1
0.6821	Remote Similarity	NPD3052	Approved
0.6821	Remote Similarity	NPD3054	Approved
0.6821	Remote Similarity	NPD5946	Clinical (unspecified phase)
0.6806	Remote Similarity	NPD2584	Suspended
0.6805	Remote Similarity	NPD3909	Discontinued
0.6803	Remote Similarity	NPD5204	Approved
0.6803	Remote Similarity	NPD5736	Approved
0.68	Remote Similarity	NPD5119	Approved
0.68	Remote Similarity	NPD5121	Approved
0.68	Remote Similarity	NPD5120	Approved
0.68	Remote Similarity	NPD5837	Clinical (unspecified phase)
0.6797	Remote Similarity	NPD1522	Approved
0.6797	Remote Similarity	NPD1523	Approved
0.6797	Remote Similarity	NPD3175	Clinical (unspecified phase)
0.6797	Remote Similarity	NPD6032	Approved
0.6786	Remote Similarity	NPD5292	Approved
0.6786	Remote Similarity	NPD5291	Approved
0.6783	Remote Similarity	NPD3847	Discontinued
0.6779	Remote Similarity	NPD598	Approved
0.6779	Remote Similarity	NPD601	Approved
0.6779	Remote Similarity	NPD597	Approved
0.6776	Remote Similarity	NPD1536	Approved
0.6766	Remote Similarity	NPD4652	Approved
0.6761	Remote Similarity	NPD4105	Approved
0.6761	Remote Similarity	NPD4102	Approved
0.6761	Remote Similarity	NPD4209	Clinical (unspecified phase)
0.6755	Remote Similarity	NPD6355	Discontinued
0.6753	Remote Similarity	NPD6809	Clinical (unspecified phase)
0.6752	Remote Similarity	NPD6667	Approved
0.6752	Remote Similarity	NPD6666	Approved
0.675	Remote Similarity	NPD3687	Approved
0.675	Remote Similarity	NPD3686	Approved
0.675	Remote Similarity	NPD4003	Phase 3
0.6748	Remote Similarity	NPD3465	Clinical (unspecified phase)
0.6747	Remote Similarity	NPD6746	Phase 2
0.6739	Remote Similarity	NPD821	Approved
0.6733	Remote Similarity	NPD840	Approved
0.6733	Remote Similarity	NPD1136	Approved
0.6733	Remote Similarity	NPD839	Approved
0.6733	Remote Similarity	NPD1130	Approved
0.6733	Remote Similarity	NPD6405	Approved
0.6733	Remote Similarity	NPD6407	Approved
0.6733	Remote Similarity	NPD1132	Approved
0.6732	Remote Similarity	NPD6865	Phase 2
0.6732	Remote Similarity	NPD6864	Phase 2
0.6731	Remote Similarity	NPD6331	Phase 2
0.6728	Remote Similarity	NPD7615	Clinical (unspecified phase)
0.6727	Remote Similarity	NPD8070	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