NPASS Compound

Structure

NPC3812 OpenBabel06302215132D 35 37 0 0 1 0 0 0 0 0999 V2000 2.5981 -2.5000 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 -1.0000 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 0.8660 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -1.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8660 -1.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.7321 -1.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.7321 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8660 0.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8660 1.5000 0.0000 O 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 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 4.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9282 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9282 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7942 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.6603 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.6603 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7942 3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.5263 3.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -9.5263 1.5000 0.0000 O 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 -1.7321 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 3.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 4.5000 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 -2.5981 0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 2 4 1 0 0 0 0 4 5 1 0 0 0 0 6 5 1 6 0 0 0 6 7 1 0 0 0 0 6 32 1 0 0 0 0 7 8 1 0 0 0 0 7 35 1 1 0 0 0 8 9 1 0 0 0 0 8 34 1 6 0 0 0 9 10 1 0 0 0 0 9 33 1 1 0 0 0 10 11 1 6 0 0 0 10 32 1 0 0 0 0 11 12 1 0 0 0 0 12 29 2 0 0 0 0 12 13 1 0 0 0 0 13 14 2 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 15 28 2 0 0 0 0 16 17 2 0 0 0 0 16 18 1 0 0 0 0 18 19 2 0 0 0 0 19 20 1 0 0 0 0 20 25 2 0 0 0 0 20 21 1 0 0 0 0 21 22 2 0 0 0 0 22 23 1 0 0 0 0 23 24 2 0 0 0 0 23 27 1 0 0 0 0 24 25 1 0 0 0 0 24 26 1 0 0 0 0 28 29 1 0 0 0 0 28 31 1 0 0 0 0 29 30 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	235.12
Volume:	243.113
LogP:	1.587
LogD:	1.355
LogS:	-2.777
# Rotatable Bonds:	3
TPSA:	76.48
# H-Bond Aceptor:	4
# H-Bond Donor:	4
# Rings:	2
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.652
Synthetic Accessibility Score:	3.195
Fsp3:	0.385
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.695
MDCK Permeability:	5.701699592464138e-06
Pgp-inhibitor:	0.001
Pgp-substrate:	0.383
Human Intestinal Absorption (HIA):	0.013
20% Bioavailability (F20%):	0.257
30% Bioavailability (F30%):	0.051

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.182
Plasma Protein Binding (PPB):	57.73567581176758%
Volume Distribution (VD):	1.123
Pgp-substrate:	44.974143981933594%

ADMET: Metabolism

CYP1A2-inhibitor:	0.237
CYP1A2-substrate:	0.172
CYP2C19-inhibitor:	0.064
CYP2C19-substrate:	0.08
CYP2C9-inhibitor:	0.035
CYP2C9-substrate:	0.902
CYP2D6-inhibitor:	0.044
CYP2D6-substrate:	0.766
CYP3A4-inhibitor:	0.013
CYP3A4-substrate:	0.214

ADMET: Excretion

Clearance (CL):	9.728
Half-life (T1/2):	0.678

ADMET: Toxicity

hERG Blockers:	0.038
Human Hepatotoxicity (H-HT):	0.253
Drug-inuced Liver Injury (DILI):	0.361
AMES Toxicity:	0.153
Rat Oral Acute Toxicity:	0.934
Maximum Recommended Daily Dose:	0.957
Skin Sensitization:	0.17
Carcinogencity:	0.27
Eye Corrosion:	0.007
Eye Irritation:	0.8
Respiratory Toxicity:	0.818

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

Natural Product: NPC3812

Natural Product ID:	NPC3812
*Common Name:**	PLCKXYSWZCDSJH-NYUCKZKASA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	PLCKXYSWZCDSJH-NYUCKZKASA-N
Standard InCHI:	InChI=1S/C23H24O12/c1-10(24)33-9-17-20(30)21(31)22(32)23(35-17)34-16-7-4-12(18(28)19(16)29)13(25)5-2-11-3-6-14(26)15(27)8-11/h2-8,17,20-23,26-32H,9H2,1H3/b5-2+/t17-,20-,21+,22-,23-/m1/s1
SMILES:	CC(=O)OC[C@@H]1[C@H]([C@@H]([C@H]([C@H](Oc2ccc(C(=O)/C=C/c3ccc(c(c3)O)O)c(c2O)O)O1)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	14213555
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0001111] Flavonoid glycosides [CHEMONTID:0001583] Flavonoid O-glycosides

*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
NPO23108	Pinus flexilis	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[9834165]
NPO20454	Bidens pilosa	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[469551]
NPO23440	Aconitum napellus	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23876370]
NPO24718	Streptomyces parvulus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	PMID[23423168]
NPO15117	Chromolaena odorata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23186307]
NPO24588	Phellinus igniarius	Species	Hymenochaetaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20583752]
NPO23924	Psilotum nudum	Species	Psilotaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20488581]
NPO24811	Cibotium barometz	Species	Cibotiaceae	Eukaryota	rhizomes	n.a.	n.a.	PMID[19739599]
NPO9392	Elaeodendron alluaudianum	Species	Celastraceae	Eukaryota	n.a.	Madagascar Rainforest	n.a.	PMID[19058971]
NPO9392	Elaeodendron alluaudianum	Species	Celastraceae	Eukaryota	n.a.	stem	n.a.	PMID[19058971]

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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
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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

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
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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 NPC3812 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	372
0.1-0.2	1602
0.2-0.3	3873
0.3-0.4	8387
0.4-0.5	9399
0.5-0.6	4286
0.6-0.7	4782
0.7-0.8	5764
0.8-0.85	2572
0.85-0.9	1276
0.9-0.95	356
0.95-1	28

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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 NPC3812 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	331
0.1-0.2	897
0.2-0.3	1925
0.3-0.4	2566
0.4-0.5	1858
0.5-0.6	963
0.6-0.7	405
0.7-0.8	151
0.8-0.85	34
0.85-0.9	15
0.9-0.95	5
0.95-1	0

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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