NPASS Compound

Structure

NPC33690 OpenBabel06302216192D 43 47 0 0 1 0 0 0 0 0999 V2000 6.9282 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7942 -0.5000 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 6.9282 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 -0.5000 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 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 1.7321 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -0.5000 0.0000 C 0 0 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 0.0000 -2.0000 0.0000 C 0 0 1 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 -0.8660 -0.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.7321 -0.0000 0.0000 O 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 -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 -4.3301 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2812 -1.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.5902 -2.7601 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.8690 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.8690 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.3690 -0.1340 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.8690 0.7321 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.3690 1.5981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.3690 1.5981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.8690 0.7321 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.3690 -0.1340 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.8690 0.7321 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.8690 2.4641 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.2812 -0.1910 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -0.5000 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 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 -1.7321 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 8.6603 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 6 2 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 4 1 0 0 0 0 3 43 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 6 7 1 0 0 0 0 7 8 2 0 0 0 0 8 9 1 0 0 0 0 9 10 2 0 0 0 0 9 11 1 0 0 0 0 11 12 1 0 0 0 0 13 12 1 6 0 0 0 13 14 1 0 0 0 0 13 39 1 0 0 0 0 14 15 1 0 0 0 0 14 42 1 1 0 0 0 15 16 1 0 0 0 0 15 41 1 6 0 0 0 16 17 1 0 0 0 0 16 40 1 1 0 0 0 17 18 1 6 0 0 0 17 39 1 0 0 0 0 18 19 1 0 0 0 0 19 37 2 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 21 22 1 0 0 0 0 22 36 2 0 0 0 0 22 23 1 0 0 0 0 23 24 2 0 0 0 0 23 25 1 0 0 0 0 25 26 2 0 0 0 0 25 35 1 0 0 0 0 26 27 1 0 0 0 0 27 32 2 0 0 0 0 27 28 1 0 0 0 0 28 29 2 0 0 0 0 29 30 1 0 0 0 0 30 31 2 0 0 0 0 30 34 1 0 0 0 0 31 32 1 0 0 0 0 31 33 1 0 0 0 0 35 36 1 0 0 0 0 36 37 1 0 0 0 0 37 38 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	594.14
Volume:	564.653
LogP:	2.378
LogD:	1.219
LogS:	-3.962
# Rotatable Bonds:	8
TPSA:	212.67
# H-Bond Aceptor:	13
# H-Bond Donor:	7
# Rings:	5
# Heavy Atoms:	13

MedChem Properties

QED Drug-Likeness Score:	0.118
Synthetic Accessibility Score:	4.25
Fsp3:	0.2
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	2
PAINS Alert:	1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.42
MDCK Permeability:	3.0459761546808295e-05
Pgp-inhibitor:	0.056
Pgp-substrate:	0.535
Human Intestinal Absorption (HIA):	0.356
20% Bioavailability (F20%):	0.998
30% Bioavailability (F30%):	0.997

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.028
Plasma Protein Binding (PPB):	101.35638427734375%
Volume Distribution (VD):	0.42
Pgp-substrate:	1.0668002367019653%

ADMET: Metabolism

CYP1A2-inhibitor:	0.441
CYP1A2-substrate:	0.018
CYP2C19-inhibitor:	0.178
CYP2C19-substrate:	0.049
CYP2C9-inhibitor:	0.663
CYP2C9-substrate:	0.308
CYP2D6-inhibitor:	0.314
CYP2D6-substrate:	0.173
CYP3A4-inhibitor:	0.226
CYP3A4-substrate:	0.1

ADMET: Excretion

Clearance (CL):	4.619
Half-life (T1/2):	0.906

ADMET: Toxicity

hERG Blockers:	0.076
Human Hepatotoxicity (H-HT):	0.261
Drug-inuced Liver Injury (DILI):	0.391
AMES Toxicity:	0.765
Rat Oral Acute Toxicity:	0.637
Maximum Recommended Daily Dose:	0.828
Skin Sensitization:	0.956
Carcinogencity:	0.383
Eye Corrosion:	0.003
Eye Irritation:	0.595
Respiratory Toxicity:	0.017

Download Data

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

Natural Product: NPC33690

Natural Product ID:	NPC33690
*Common Name:**	JEBDJWVQHWVRFP-BZCZOPFFSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	JEBDJWVQHWVRFP-BZCZOPFFSA-N
Standard InCHI:	InChI=1S/C30H26O13/c31-16-5-1-14(2-6-16)4-10-23(34)40-13-22-25(36)27(38)28(39)30(43-22)42-20-9-7-17-24(35)21(41-29(17)26(20)37)12-15-3-8-18(32)19(33)11-15/h1-12,22,25,27-28,30-33,36-39H,13H2/b10-4+,21-12-/t22-,25-,27+,28-,30-/m1/s1
SMILES:	c1cc(ccc1/C=C/C(=O)OC[C@@H]1[C@H]([C@@H]([C@H]([C@H](Oc2ccc3C(=O)/C(=C/c4ccc(c(c4)O)O)/Oc3c2O)O1)O)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	15071009
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0001111] Flavonoid glycosides [CHEMONTID:0001583] Flavonoid O-glycosides [CHEMONTID:0001738] Aurone 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 NPC33690 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	416
0.1-0.2	1739
0.2-0.3	4176
0.3-0.4	8915
0.4-0.5	8869
0.5-0.6	4433
0.6-0.7	5189
0.7-0.8	5710
0.8-0.85	1978
0.85-0.9	829
0.9-0.95	423
0.95-1	20

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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 NPC33690 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	370
0.1-0.2	924
0.2-0.3	1986
0.3-0.4	2629
0.4-0.5	1823
0.5-0.6	911
0.6-0.7	343
0.7-0.8	116
0.8-0.85	30
0.85-0.9	14
0.9-0.95	4
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