NPASS Compound

Structure

NPC282633 OpenBabel06302215542D 38 42 0 0 1 0 0 0 0 0999 V2000 10.4873 4.7611 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.5092 4.9690 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 8.8401 4.2259 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.8619 4.4338 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.1928 3.6907 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.5018 2.7396 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.4800 2.5317 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.1491 3.2748 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.1272 3.0669 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.2146 3.8986 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.5455 3.1554 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.8545 2.2044 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.8327 1.9965 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.1854 1.4612 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.2072 1.6691 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.4641 1.0000 0.0000 C 0 0 2 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 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 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 1.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.5981 1.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.8060 2.4781 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.8065 2.4447 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2779 3.2935 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.8005 2.5827 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.2127 3.3917 0.0000 O 0 0 0 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 -0.0000 1.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8660 1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.7321 1.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.7321 -0.0000 0.0000 C 0 0 1 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 -0.8660 -1.5000 0.0000 C 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 -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 1 0 0 0 0 3 8 2 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 5 10 1 0 0 0 0 6 7 2 0 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 10 11 2 3 0 0 0 11 12 1 0 0 0 0 12 13 2 0 0 0 0 12 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 15 25 1 0 0 0 0 16 17 1 0 0 0 0 16 21 1 0 0 0 0 17 18 2 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 1 0 0 0 0 20 27 1 0 0 0 0 21 22 1 0 0 0 0 22 26 1 0 0 0 0 22 23 1 0 0 0 0 22 25 1 0 0 0 0 23 24 1 0 0 0 0 25 26 1 0 0 0 0 28 27 1 6 0 0 0 28 29 1 0 0 0 0 28 35 1 0 0 0 0 29 30 1 0 0 0 0 29 38 1 1 0 0 0 30 31 1 0 0 0 0 30 37 1 6 0 0 0 31 32 1 0 0 0 0 31 36 1 1 0 0 0 32 33 1 6 0 0 0 32 35 1 0 0 0 0 33 34 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	365.18
Volume:	370.623
LogP:	2.487
LogD:	0.838
LogS:	-2.171
# Rotatable Bonds:	8
TPSA:	82.14
# H-Bond Aceptor:	7
# H-Bond Donor:	0
# Rings:	2
# Heavy Atoms:	7

MedChem Properties

QED Drug-Likeness Score:	0.417
Synthetic Accessibility Score:	4.95
Fsp3:	0.632
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:	-4.717
MDCK Permeability:	6.207868864294142e-05
Pgp-inhibitor:	0.995
Pgp-substrate:	0.004
Human Intestinal Absorption (HIA):	0.011
20% Bioavailability (F20%):	0.718
30% Bioavailability (F30%):	0.976

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.537
Plasma Protein Binding (PPB):	39.16795349121094%
Volume Distribution (VD):	1.709
Pgp-substrate:	44.167015075683594%

ADMET: Metabolism

CYP1A2-inhibitor:	0.056
CYP1A2-substrate:	0.116
CYP2C19-inhibitor:	0.586
CYP2C19-substrate:	0.822
CYP2C9-inhibitor:	0.846
CYP2C9-substrate:	0.093
CYP2D6-inhibitor:	0.904
CYP2D6-substrate:	0.313
CYP3A4-inhibitor:	0.934
CYP3A4-substrate:	0.61

ADMET: Excretion

Clearance (CL):	9.282
Half-life (T1/2):	0.67

ADMET: Toxicity

hERG Blockers:	0.055
Human Hepatotoxicity (H-HT):	0.93
Drug-inuced Liver Injury (DILI):	0.576
AMES Toxicity:	0.329
Rat Oral Acute Toxicity:	0.047
Maximum Recommended Daily Dose:	0.989
Skin Sensitization:	0.978
Carcinogencity:	0.316
Eye Corrosion:	0.298
Eye Irritation:	0.419
Respiratory Toxicity:	0.94

Download Data

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

Natural Product: NPC282633

Natural Product ID:	NPC282633
*Common Name:**	RMSKZOXJAHOIER-KZOWKLRMSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	RMSKZOXJAHOIER-KZOWKLRMSA-N
Standard InCHI:	InChI=1S/C25H30O13/c1-33-14-8-11(2-4-13(14)28)3-5-16(29)36-21-12-6-7-34-23(17(12)25(10-27)22(21)38-25)37-24-20(32)19(31)18(30)15(9-26)35-24/h2-8,12,15,17-24,26-28,30-32H,9-10H2,1H3/t12-,15-,17-,18-,19+,20-,21+,22+,23+,24+,25-/m1/s1
SMILES:	COc1cc(ccc1O)C=CC(=O)O[C@H]1[C@@H]2C=CO[C@H]([C@@H]2[C@]2(CO)[C@H]1O2)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000476] Cinnamic acids and derivatives [CHEMONTID:0001391] Hydroxycinnamic acids and derivatives [CHEMONTID:0000059] Coumaric acids and derivatives

*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
NPO12175	Iostephane heterophylla	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11473422]
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]
NPO1150	Juncus effusus	Species	Juncaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[30892891]
NPO1150	Juncus effusus	Species	Juncaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO1150	Juncus effusus	Species	Juncaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
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]
NPO1150	Juncus effusus	Species	Juncaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO9908	Adenium somalense	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12175	Iostephane heterophylla	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1790	Plectranthus comosus	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13466	Atroxima afzeliana	Species	Polygalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3432	Tovomita brasiliensis	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9550	Eritrichium incanum	Species	Boraginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14254	Kandelia candel	Species	Rhizophoraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11255	Veronica thomsonii	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1314	Goodenia strophiolata	Species	Goodeniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11491	Vellozia declinans	Species	Velloziaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1150	Juncus effusus	Species	Juncaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14462	Jasonia tuberosa	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5908	Dianella tasmanica	Species	Asphodelaceae	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

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

☑ 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 NPC282633 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	349
0.1-0.2	1444
0.2-0.3	3383
0.3-0.4	8092
0.4-0.5	10172
0.5-0.6	8307
0.6-0.7	8605
0.7-0.8	2114
0.8-0.85	171
0.85-0.9	43
0.9-0.95	12
0.95-1	5

Similarity Score	Similarity Level	Natural Product ID

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 NPC282633 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	276
0.1-0.2	836
0.2-0.3	1989
0.3-0.4	2801
0.4-0.5	1929
0.5-0.6	1000
0.6-0.7	294
0.7-0.8	24
0.8-0.85	0
0.85-0.9	0
0.9-0.95	1
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage

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