NPASS Compound

Structure

CID21184 OpenBabel06191715342D 30 33 0 0 1 0 0 0 0 0999 V2000 -1.7321 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.5981 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -0.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.7321 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 1.0000 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 25 1 0 0 0 0 2 26 1 0 0 0 0 3 27 1 0 0 0 0 4 5 2 0 0 0 0 4 10 1 0 0 0 0 5 16 1 0 0 0 0 6 10 2 0 0 0 0 6 14 1 0 0 0 0 7 11 2 0 0 0 0 7 12 1 0 0 0 0 8 11 1 0 0 0 0 8 13 2 0 0 0 0 9 22 1 0 0 0 0 10 19 1 0 0 0 0 12 17 2 0 0 0 0 12 25 1 0 0 0 0 13 17 1 0 0 0 0 13 26 1 0 0 0 0 14 20 2 0 0 0 0 14 27 1 0 0 0 0 15 9 1 1 0 0 0 15 18 1 0 0 0 0 15 28 1 0 0 0 0 16 23 2 0 0 0 0 16 29 1 0 0 0 0 17 24 1 0 0 0 0 18 11 1 6 0 0 0 18 30 1 0 0 0 0 19 21 2 0 0 0 0 19 29 1 0 0 0 0 20 21 1 0 0 0 0 20 28 1 0 0 0 0 21 30 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	416.11
Volume:	395.567
LogP:	1.629
LogD:	1.739
LogS:	-4.199
# Rotatable Bonds:	5
TPSA:	116.82
# H-Bond Aceptor:	9
# H-Bond Donor:	2
# Rings:	4
# Heavy Atoms:	9

MedChem Properties

QED Drug-Likeness Score:	0.605
Synthetic Accessibility Score:	3.511
Fsp3:	0.286
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	1
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.882
MDCK Permeability:	3.331883635837585e-05
Pgp-inhibitor:	0.754
Pgp-substrate:	0.001
Human Intestinal Absorption (HIA):	0.014
20% Bioavailability (F20%):	0.003
30% Bioavailability (F30%):	0.033

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.474
Plasma Protein Binding (PPB):	67.92041015625%
Volume Distribution (VD):	0.853
Pgp-substrate:	30.291362762451172%

ADMET: Metabolism

CYP1A2-inhibitor:	0.063
CYP1A2-substrate:	0.896
CYP2C19-inhibitor:	0.055
CYP2C19-substrate:	0.669
CYP2C9-inhibitor:	0.239
CYP2C9-substrate:	0.735
CYP2D6-inhibitor:	0.107
CYP2D6-substrate:	0.583
CYP3A4-inhibitor:	0.584
CYP3A4-substrate:	0.783

ADMET: Excretion

Clearance (CL):	12.393
Half-life (T1/2):	0.69

ADMET: Toxicity

hERG Blockers:	0.359
Human Hepatotoxicity (H-HT):	0.71
Drug-inuced Liver Injury (DILI):	0.944
AMES Toxicity:	0.062
Rat Oral Acute Toxicity:	0.364
Maximum Recommended Daily Dose:	0.161
Skin Sensitization:	0.9
Carcinogencity:	0.305
Eye Corrosion:	0.003
Eye Irritation:	0.034
Respiratory Toxicity:	0.02

Download Data

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

Natural Product: NPC21184

Natural Product ID:	NPC21184
*Common Name:**	Cleomiscosin D
IUPAC Name:	(2S,3S)-2-(4-hydroxy-3,5-dimethoxyphenyl)-3-(hydroxymethyl)-5-methoxy-2,3-dihydropyrano[3,2-h][1,4]benzodioxin-9-one
Synonyms:	Cleomiscosin D
Standard InCHIKey:	IXSZNNRKGDOXQI-YJBOKZPZSA-N
Standard InCHI:	InChI=1S/C21H20O9/c1-25-12-7-11(8-13(26-2)17(12)24)18-15(9-22)28-20-14(27-3)6-10-4-5-16(23)29-19(10)21(20)30-18/h4-8,15,18,22,24H,9H2,1-3H3/t15-,18-/m0/s1
SMILES:	COc1cc(cc(c1O)OC)[C@H]1[C@H](CO)Oc2c(cc3ccc(=O)oc3c2O1)OC
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL256915
PubChem CID:	13965876
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0001392] Lignans, neolignans and related compounds [CHEMONTID:0002545] Coumarinolignans

*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

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Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO29000	Nephila clavata	Species	Nephilidae	Eukaryota	n.a.	n.a.	n.a.	PMID[21188966]
NPO28941	Pogonopus speciosus	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[1982768]
NPO18723	Zanthoxylum avicennae	Species	Rutaceae	Eukaryota	stem wood	Pakuashan, Changhua County, Taiwan	2006-Jun	PMID[18211005]
NPO29062	Hibiscus syriacus	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11575966]
NPO28697	Talaromyces convolutus	Species	Trichocomaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[10869198]
NPO29062	Hibiscus syriacus	Species	Malvaceae	Eukaryota	n.a.	root	n.a.	PMID[10617409]
NPO28941	Pogonopus speciosus	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[10514334]
NPO29062	Hibiscus syriacus	Species	Malvaceae	Eukaryota	root bark	n.a.	n.a.	PMID[10346965]
NPO28697	Talaromyces convolutus	Species	Trichocomaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28835	Gentianella nitida	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]

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☑ 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

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Organism ID	NP ID	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference
No data available in table

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☑ 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	3

Activity Type	# Activity
NON-MOLECULAR	2
Subcellular	1

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT1084	Subcellular	Liver microsomes	Rattus norvegicus	IC50	=	5.5	ug.mL-1	PMID[492586]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	IC50	>	50000.0	nM	PMID[492585]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	IC50	=	13080.0	nM	PMID[492585]

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☑ 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 NPC21184 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	407
0.1-0.2	1818
0.2-0.3	4832
0.3-0.4	9844
0.4-0.5	7872
0.5-0.6	4004
0.6-0.7	5307
0.7-0.8	4984
0.8-0.85	1872
0.85-0.9	1465
0.9-0.95	270
0.95-1	22

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Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC294522
1.0	High Similarity	NPC205727
1.0	High Similarity	NPC120426
0.993	High Similarity	NPC30688
0.993	High Similarity	NPC176903

Showing 1 to 5 of 200 entries

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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 NPC21184 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	377
0.1-0.2	972
0.2-0.3	2059
0.3-0.4	2589
0.4-0.5	1741
0.5-0.6	916
0.6-0.7	337
0.7-0.8	109
0.8-0.85	27
0.85-0.9	19
0.9-0.95	4
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.9252	High Similarity	NPD1653	Approved
0.8671	High Similarity	NPD1613	Approved
0.8671	High Similarity	NPD1612	Clinical (unspecified phase)
0.859	High Similarity	NPD4868	Clinical (unspecified phase)
0.8462	Intermediate Similarity	NPD3027	Phase 3

Showing 1 to 5 of 200 entries

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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