NPASS Compound

Structure

NPC102899 OpenBabel06302215192D 25 27 0 0 1 0 0 0 0 0999 V2000 -4.3301 -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 -3.4641 -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 -4.3301 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 2.0000 0.0000 C 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 -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 -3.4641 3.0000 0.0000 O 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 -2.5981 1.5000 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 -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 C 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 1.7321 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 1 2 1 0 0 0 0 2 3 1 0 0 0 0 3 13 2 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 11 1 0 0 0 0 5 6 1 0 0 0 0 6 7 2 0 0 0 0 7 8 1 0 0 0 0 8 9 2 0 0 0 0 8 10 1 0 0 0 0 10 11 1 0 0 0 0 11 12 2 0 0 0 0 12 13 1 0 0 0 0 13 14 1 0 0 0 0 15 14 1 6 0 0 0 15 16 1 0 0 0 0 15 22 1 0 0 0 0 16 17 1 0 0 0 0 16 25 1 1 0 0 0 17 18 1 0 0 0 0 17 24 1 6 0 0 0 18 19 1 0 0 0 0 18 23 1 1 0 0 0 19 20 1 6 0 0 0 19 22 1 0 0 0 0 20 21 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	354.1
Volume:	325.553
LogP:	-0.264
LogD:	-0.396
LogS:	-1.743
# Rotatable Bonds:	4
TPSA:	138.82
# H-Bond Aceptor:	9
# H-Bond Donor:	4
# Rings:	3
# Heavy Atoms:	9

MedChem Properties

QED Drug-Likeness Score:	0.508
Synthetic Accessibility Score:	3.61
Fsp3:	0.438
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:	-5.745
MDCK Permeability:	3.658165951492265e-05
Pgp-inhibitor:	0.001
Pgp-substrate:	0.941
Human Intestinal Absorption (HIA):	0.321
20% Bioavailability (F20%):	0.037
30% Bioavailability (F30%):	0.975

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.342
Plasma Protein Binding (PPB):	46.5645637512207%
Volume Distribution (VD):	0.666
Pgp-substrate:	33.83216094970703%

ADMET: Metabolism

CYP1A2-inhibitor:	0.102
CYP1A2-substrate:	0.579
CYP2C19-inhibitor:	0.024
CYP2C19-substrate:	0.239
CYP2C9-inhibitor:	0.002
CYP2C9-substrate:	0.393
CYP2D6-inhibitor:	0.017
CYP2D6-substrate:	0.393
CYP3A4-inhibitor:	0.007
CYP3A4-substrate:	0.051

ADMET: Excretion

Clearance (CL):	5.057
Half-life (T1/2):	0.657

ADMET: Toxicity

hERG Blockers:	0.181
Human Hepatotoxicity (H-HT):	0.231
Drug-inuced Liver Injury (DILI):	0.69
AMES Toxicity:	0.298
Rat Oral Acute Toxicity:	0.052
Maximum Recommended Daily Dose:	0.01
Skin Sensitization:	0.232
Carcinogencity:	0.705
Eye Corrosion:	0.005
Eye Irritation:	0.097
Respiratory Toxicity:	0.021

Download Data

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

Natural Product: NPC102899

Natural Product ID:	NPC102899
*Common Name:**	SGTCGCCQZOUMJJ-SLZITWOASA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	SGTCGCCQZOUMJJ-SLZITWOASA-N
Standard InCHI:	InChI=1S/C16H18O9/c1-22-9-4-7-2-3-12(18)23-8(7)5-10(9)24-16-15(21)14(20)13(19)11(6-17)25-16/h2-5,11,13-17,19-21H,6H2,1H3/t11-,13-,14+,15-,16-/m0/s1
SMILES:	COc1cc2ccc(=O)oc2cc1O[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:	1152160
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000145] Coumarins and derivatives [CHEMONTID:0001743] Coumarin 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

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO8246	Lantana involucrata	Species	Verbenaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15217280]
NPO4890	Streptomyces rimosus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	PMID[17631493]
NPO13607	Arenaria kansuensis	Species	Scolopacidae	Eukaryota	n.a.	n.a.	n.a.	PMID[17655145]
NPO4890	Streptomyces rimosus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	PMID[1833366]
NPO9032	Geotrichum candidum	Species	Dipodascaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20488699]
NPO14190	Streptopelia orientalis	Species	Columbidae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO13305	Mammea africana	Species	Calophyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO13305	Mammea africana	Species	Calophyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO14190	Streptopelia orientalis	Species	Columbidae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO13607	Arenaria kansuensis	Species	Scolopacidae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO7350	Sitotroga cerealella	Species	Gelechiidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8246	Lantana involucrata	Species	Verbenaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13305	Mammea africana	Species	Calophyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13201	Diphasiastrum tristachyum	Species	Lycopodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6418	Passalora rosicola	Species	Mycosphaerellaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14882	Collariella gracilis	Species	Chaetomiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5412	Tedania anhelans	Species	Tedaniidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16116	Aniba canelilla	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14190	Streptopelia orientalis	Species	Columbidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8655	Wendlandia tinctoria	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7119	Endospermum diadenum	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2510	Pteris argentea	Species	Pteridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23040	Methylomonas methanica	Species	Methylococcaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO19165	Comptonia peregrina	Species	Myricaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16769	Baccharis hutchisonii	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4890	Streptomyces rimosus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO6089	Metacalypogeia alternifolia	Species	Calypogeiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9032	Geotrichum candidum	Species	Dipodascaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19510	Origanum floribundum	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11341	Eucalyptus piperita	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13607	Arenaria kansuensis	Species	Scolopacidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13497	Senecio trichopterygius	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13937	Leptodontidium elatius	Species	n.a.	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14708	Macowania corymbosa	Species	Asteraceae	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 NPC102899 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	397
0.1-0.2	1814
0.2-0.3	4362
0.3-0.4	9727
0.4-0.5	8548
0.5-0.6	4224
0.6-0.7	5426
0.7-0.8	5434
0.8-0.85	1989
0.85-0.9	686
0.9-0.95	84
0.95-1	6

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 NPC102899 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	364
0.1-0.2	942
0.2-0.3	2059
0.3-0.4	2663
0.4-0.5	1785
0.5-0.6	886
0.6-0.7	290
0.7-0.8	126
0.8-0.85	25
0.85-0.9	8
0.9-0.95	1
0.95-1	1

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