NPASS Compound

Structure

NPC34875 OpenBabel06302215152D 51 60 0 0 1 0 0 0 0 0999 V2000 4.4716 -0.1349 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9441 -0.9533 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4716 -1.7716 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5267 -1.7716 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0542 -0.9533 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5267 -0.1349 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5818 1.5018 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.6420 1.6005 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.2544 1.0670 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5668 0.7094 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4820 0.2422 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0638 0.0171 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6272 0.2038 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6272 0.8632 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 1.0670 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.3876 1.6005 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8243 1.4139 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2425 1.6389 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3272 2.1062 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0148 2.4638 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3876 2.2600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 2.7935 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.6272 2.9973 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6272 3.9423 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4455 4.4147 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2639 3.9423 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2639 2.9973 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4455 2.5248 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9661 2.3650 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.4455 6.3046 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.3876 3.3270 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.0956 4.2257 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7279 4.9280 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4359 5.8267 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4884 6.0231 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1207 5.3209 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8287 4.4222 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7804 6.9218 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.0148 3.1233 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.0069 1.0835 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.3876 0.5335 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.2775 0.5335 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7500 -0.2848 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6949 -0.2848 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1674 0.5335 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6949 1.3519 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7500 1.3519 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1123 0.5335 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 2.2465 -0.3132 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.9441 -2.5899 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 51 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 7 6 1 6 0 0 0 7 8 1 0 0 0 0 7 29 1 0 0 0 0 8 9 1 1 0 0 0 8 28 1 0 0 0 0 9 14 2 0 0 0 0 9 10 1 0 0 0 0 10 11 2 0 0 0 0 11 12 1 0 0 0 0 11 50 1 0 0 0 0 12 13 2 0 0 0 0 13 49 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 41 1 0 0 0 0 16 21 2 0 0 0 0 16 17 1 0 0 0 0 17 18 2 0 0 0 0 18 19 1 0 0 0 0 18 40 1 0 0 0 0 19 20 2 0 0 0 0 20 39 1 0 0 0 0 20 21 1 0 0 0 0 22 21 1 1 0 0 0 22 23 1 0 0 0 0 22 31 1 0 0 0 0 23 28 2 0 0 0 0 23 24 1 0 0 0 0 24 25 2 0 0 0 0 25 26 1 0 0 0 0 25 30 1 0 0 0 0 26 27 2 0 0 0 0 27 28 1 0 0 0 0 27 29 1 0 0 0 0 31 32 1 6 0 0 0 31 39 1 0 0 0 0 32 37 2 0 0 0 0 32 33 1 0 0 0 0 33 34 2 0 0 0 0 34 35 1 0 0 0 0 35 36 2 0 0 0 0 35 38 1 0 0 0 0 36 37 1 0 0 0 0 41 42 1 1 0 0 0 41 49 1 0 0 0 0 42 47 2 0 0 0 0 42 43 1 0 0 0 0 43 44 2 0 0 0 0 44 45 1 0 0 0 0 45 46 2 0 0 0 0 45 48 1 0 0 0 0 46 47 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	678.19
Volume:	681.079
LogP:	7.161
LogD:	4.074
LogS:	-4.198
# Rotatable Bonds:	3
TPSA:	149.07
# H-Bond Aceptor:	9
# H-Bond Donor:	6
# Rings:	10
# Heavy Atoms:	9

MedChem Properties

QED Drug-Likeness Score:	0.109
Synthetic Accessibility Score:	4.807
Fsp3:	0.143
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.877
MDCK Permeability:	9.489647709415294e-06
Pgp-inhibitor:	0.337
Pgp-substrate:	0.071
Human Intestinal Absorption (HIA):	0.796
20% Bioavailability (F20%):	0.043
30% Bioavailability (F30%):	0.998

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.002
Plasma Protein Binding (PPB):	94.4701919555664%
Volume Distribution (VD):	0.698
Pgp-substrate:	4.416366100311279%

ADMET: Metabolism

CYP1A2-inhibitor:	0.035
CYP1A2-substrate:	0.753
CYP2C19-inhibitor:	0.968
CYP2C19-substrate:	0.061
CYP2C9-inhibitor:	0.875
CYP2C9-substrate:	0.998
CYP2D6-inhibitor:	0.403
CYP2D6-substrate:	0.893
CYP3A4-inhibitor:	0.564
CYP3A4-substrate:	0.505

ADMET: Excretion

Clearance (CL):	10.523
Half-life (T1/2):	0.17

ADMET: Toxicity

hERG Blockers:	0.11
Human Hepatotoxicity (H-HT):	0.23
Drug-inuced Liver Injury (DILI):	0.929
AMES Toxicity:	0.567
Rat Oral Acute Toxicity:	0.972
Maximum Recommended Daily Dose:	0.974
Skin Sensitization:	0.91
Carcinogencity:	0.073
Eye Corrosion:	0.003
Eye Irritation:	0.901
Respiratory Toxicity:	0.033

Download Data

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

Natural Product: NPC34875

Natural Product ID:	NPC34875
*Common Name:**	KUTVNHOAKHJJFL-MHZVOPJQSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	KUTVNHOAKHJJFL-MHZVOPJQSA-N
Standard InCHI:	InChI=1S/C42H30O9/c43-22-7-1-19(2-8-22)40-37-28-13-25(46)17-32-35(28)39(42(50-32)21-5-11-24(45)12-6-21)30-15-27(48)18-33-36(30)38(29-14-26(47)16-31(49-40)34(29)37)41(51-33)20-3-9-23(44)10-4-20/h1-18,37-48H/t37-,38-,39+,40+,41+,42-/m0/s1
SMILES:	c1cc(ccc1[C@@H]1[C@H]2c3cc(cc4c3[C@@H](c3cc(cc5c3[C@H](c3cc(cc(c23)O1)O)[C@@H](c1ccc(cc1)O)O5)O)[C@H](c1ccc(cc1)O)O4)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	101821359
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0003405] 2-arylbenzofuran flavonoids

*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
NPO1276	Thonningia sanguinea	Species	Balanophoraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[10843586]
NPO5239	Hyrtios erecta	Species	Thorectidae	Eukaryota	n.a.	Okinawan	n.a.	PMID[11076554]
NPO11304	Vitis thunbergii	Species	Vitaceae	Eukaryota	Roots	n.a.	n.a.	PMID[15730246]
NPO5239	Hyrtios erecta	Species	Thorectidae	Eukaryota	n.a.	red sea	n.a.	PMID[16180827]
NPO5239	Hyrtios erecta	Species	Thorectidae	Eukaryota	n.a.	Red Sea	n.a.	PMID[17190441]
NPO1276	Thonningia sanguinea	Species	Balanophoraceae	Eukaryota	Subaerial Parts	n.a.	n.a.	PMID[30207720]
NPO5239	Hyrtios erecta	Species	Thorectidae	Eukaryota	n.a.	n.a.	n.a.	PMID[3572416]
NPO5239	Hyrtios erecta	Species	Thorectidae	Eukaryota	n.a.	n.a.	n.a.	PMID[8778242]
NPO5239	Hyrtios erecta	Species	Thorectidae	Eukaryota	n.a.	n.a.	n.a.	PMID[9461648]
NPO6028	Laurencia pinnatifida	Species	Rhodomelaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5899	Ainsliaea uniflora	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10086	Scrophularia scorodonia	Species	Scrophulariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9038	Aconitum burnatii	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4980	Lycopodium erythraeum	Species	Lycopodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12049	Lecania gerlachei	Species	Ramalinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1276	Thonningia sanguinea	Species	Balanophoraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10313	Plantago arborescens	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11941	Helleborus serbicus	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16596	Dysoxylum schiffneri	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5239	Hyrtios erecta	Species	Thorectidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20597	Phascolion strombus	Species	Phascolionidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO222	Phebalium drummondii	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8519	Garcinia andamanica	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11304	Vitis thunbergii	Species	Vitaceae	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 NPC34875 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	501
0.1-0.2	1783
0.2-0.3	4615
0.3-0.4	12747
0.4-0.5	5506
0.5-0.6	4796
0.6-0.7	8790
0.7-0.8	3343
0.8-0.85	425
0.85-0.9	138
0.9-0.95	39
0.95-1	14

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 NPC34875 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	421
0.1-0.2	956
0.2-0.3	1744
0.3-0.4	2772
0.4-0.5	1656
0.5-0.6	1013
0.6-0.7	517
0.7-0.8	63
0.8-0.85	5
0.85-0.9	3
0.9-0.95	0
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