NPASS Compound

Structure

NPC881 OpenBabel06302215112D 68 76 0 0 1 0 0 0 0 0999 V2000 -4.3294 0.8146 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.5769 -0.1093 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.5008 -0.3570 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.1773 0.3194 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9297 1.2433 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0058 1.4909 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.7583 2.4149 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.6062 1.9196 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.1012 0.0717 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.9005 -0.7857 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1480 -1.7096 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.2049 0.2048 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.4715 -0.4715 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.1215 -1.0779 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.1988 -0.5682 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.5838 -0.4976 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8920 -0.2563 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.0527 0.1007 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.0291 0.4914 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4204 0.4993 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6093 0.8422 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4068 1.1772 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0154 1.1693 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8266 0.8265 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4916 1.0290 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1008 1.0527 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0740 1.4029 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1418 1.7294 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5326 1.7058 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7074 1.3556 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6170 1.2399 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.0600 2.5037 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.2855 2.5852 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.2561 0.8920 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8460 1.6450 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.4976 0.5839 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.5682 0.1988 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.0779 -0.1214 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.7780 -0.1213 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.3844 -0.4714 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0607 0.2050 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.7345 -1.0777 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3279 -0.8349 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8877 -1.1474 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9924 -1.7799 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5632 -2.2561 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7345 -1.7778 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9062 -2.2562 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.0780 -2.7344 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0780 -3.6911 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9065 -4.1692 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9067 -4.8995 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.7347 -3.6910 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.9064 -3.2128 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2740 -3.5780 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.6367 -3.2127 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.3671 -4.0561 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.5630 -3.2127 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.4717 -2.3843 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2047 -3.0607 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.1216 -1.7780 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.9104 -2.0486 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.6701 -0.5971 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 -0.0258 2.8065 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.8684 2.0150 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5656 0.8614 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.9935 -0.0718 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 2 10 1 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 4 9 1 0 0 0 0 5 6 1 0 0 0 0 5 8 1 0 0 0 0 6 7 1 0 0 0 0 10 11 2 0 0 0 0 10 12 1 0 0 0 0 13 12 1 1 0 0 0 13 14 1 0 0 0 0 13 38 1 0 0 0 0 14 15 1 0 0 0 0 14 61 1 6 0 0 0 15 16 1 6 0 0 0 15 64 1 0 0 0 0 16 17 1 0 0 0 0 17 18 1 0 0 0 0 18 19 1 0 0 0 0 18 68 1 1 0 0 0 19 24 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 21 67 1 0 0 0 0 22 23 2 0 0 0 0 22 66 1 0 0 0 0 23 24 1 0 0 0 0 23 65 1 0 0 0 0 24 25 1 0 0 0 0 25 30 2 0 0 0 0 25 26 1 0 0 0 0 26 27 2 0 0 0 0 26 34 1 0 0 0 0 27 28 1 0 0 0 0 28 29 2 0 0 0 0 28 33 1 0 0 0 0 29 30 1 0 0 0 0 29 32 1 0 0 0 0 30 31 1 0 0 0 0 34 35 2 0 0 0 0 34 36 1 0 0 0 0 37 36 1 1 0 0 0 37 38 1 0 0 0 0 37 64 1 0 0 0 0 38 39 1 1 0 0 0 39 40 1 0 0 0 0 40 41 2 0 0 0 0 40 42 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 44 63 1 0 0 0 0 45 46 2 0 0 0 0 45 62 1 0 0 0 0 46 58 1 0 0 0 0 46 47 1 0 0 0 0 48 47 1 1 0 0 0 48 49 1 0 0 0 0 48 54 1 0 0 0 0 49 50 2 0 0 0 0 49 59 1 0 0 0 0 50 51 1 0 0 0 0 51 52 2 0 0 0 0 51 53 1 0 0 0 0 53 54 1 0 0 0 0 53 57 1 6 0 0 0 53 58 1 0 0 0 0 54 55 1 0 0 0 0 54 56 1 0 0 0 0 59 60 2 0 0 0 0 59 61 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	1000.52
Volume:	972.799
LogP:	1.913
LogD:	1.814
LogS:	-3.613
# Rotatable Bonds:	16
TPSA:	313.44
# H-Bond Aceptor:	20
# H-Bond Donor:	11
# Rings:	8
# Heavy Atoms:	20

MedChem Properties

QED Drug-Likeness Score:	0.074
Synthetic Accessibility Score:	6.784
Fsp3:	0.9
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:	-6.291
MDCK Permeability:	0.00020542906713671982
Pgp-inhibitor:	0.154
Pgp-substrate:	0.685
Human Intestinal Absorption (HIA):	0.973
20% Bioavailability (F20%):	0.057
30% Bioavailability (F30%):	0.998

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.075
Plasma Protein Binding (PPB):	55.35755920410156%
Volume Distribution (VD):	0.214
Pgp-substrate:	22.437742233276367%

ADMET: Metabolism

CYP1A2-inhibitor:	0.0
CYP1A2-substrate:	0.098
CYP2C19-inhibitor:	0.002
CYP2C19-substrate:	0.072
CYP2C9-inhibitor:	0.0
CYP2C9-substrate:	0.005
CYP2D6-inhibitor:	0.001
CYP2D6-substrate:	0.041
CYP3A4-inhibitor:	0.046
CYP3A4-substrate:	0.029

ADMET: Excretion

Clearance (CL):	0.563
Half-life (T1/2):	0.701

ADMET: Toxicity

hERG Blockers:	0.614
Human Hepatotoxicity (H-HT):	0.204
Drug-inuced Liver Injury (DILI):	0.076
AMES Toxicity:	0.108
Rat Oral Acute Toxicity:	0.086
Maximum Recommended Daily Dose:	0.189
Skin Sensitization:	0.758
Carcinogencity:	0.463
Eye Corrosion:	0.003
Eye Irritation:	0.007
Respiratory Toxicity:	0.969

Download Data

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

Natural Product: NPC881

Natural Product ID:	NPC881
*Common Name:**	QCCCZTBAYDERBM-XSZDUELUSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	QCCCZTBAYDERBM-XSZDUELUSA-N
Standard InCHI:	InChI=1S/C41H30O27/c42-13-1-8(2-14(43)24(13)48)34(54)65-32-30-18-7-62-35(55)9-3-15(44)25(49)28(52)20(9)21-10(4-16(45)26(50)29(21)53)37(57)67-39(63-18)33(32)66-36(56)11-5-17(46)27(51)31-22(11)23-12(38(58)64-30)6-19(47)41(61,68-31)40(23,59)60/h1-6,18,23,30,32-33,35,39,42-46,48-53,55,59-61H,7H2/t18-,23-,30+,32+,33-,35+,39-,41-/m0/s1
SMILES:	c1c(cc(c(c1O)O)O)C(=O)O[C@@H]1[C@H]2[C@@H]3CO[C@H](c4cc(c(c(c4-c4c(cc(c(c4O)O)O)C(=O)O[C@@H]([C@H]1OC(=O)c1cc(c(c4c1[C@@H]1C(=CC(=O)[C@](C1(O)O)(O)O4)C(=O)O2)O)O)O3)O)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:0000238] Tannins [CHEMONTID:0001710] Hydrolyzable tannins

*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
NPO6039	Aglaia laxiflora	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[10785416]
NPO8621	Cylindrospermopsis raciborskii	Species	Aphanizomenonaceae	Bacteria	n.a.	n.a.	n.a.	PMID[11223086]
NPO9973	Euphorbia turczaninowii	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11520228]
NPO8621	Cylindrospermopsis raciborskii	Species	Aphanizomenonaceae	Bacteria	n.a.	n.a.	n.a.	PMID[14559084]
NPO7381	Ircinia spinosula	Species	Irciniidae	Eukaryota	n.a.	Bay of Naples, Italy	n.a.	PMID[7714539]
NPO5065	Cladonia fallax	Species	Cladoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO9734	Vincetoxicum hirundinaria	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO5065	Cladonia fallax	Species	Cladoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO9207	Styrax ferrugineus	Species	Styracaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO9207	Styrax ferrugineus	Species	Styracaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9734	Vincetoxicum hirundinaria	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8909	Pteris radiata	Species	Pteridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7625	Scopolia hladnikiana	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3119	Cephalaria uralensis	Species	Caprifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO762	Digitalis isabelliana	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5065	Cladonia fallax	Species	Cladoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8437	Encyothalia cliftonii	Species	Sporochnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7381	Ircinia spinosula	Species	Irciniidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2174	Polysiphonia elongata	Species	Rhodomelaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO550	Callicarpa maingayi	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7013	Dicoma capensis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8621	Cylindrospermopsis raciborskii	Species	Aphanizomenonaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO5301	Haplophyllum ferganicum	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15448	Chrysothamnus parryi	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4073	Geranium sylvaticum	Species	Geraniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9973	Euphorbia turczaninowii	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3924	Penicillium alutaceum	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5541	Crotalaria aegyptiaca	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2723	Artemisia carvifolia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26170	Haliclona mucosa	Species	Chalinidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8773	Sonchus ortunoi	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6039	Aglaia laxiflora	Species	Meliaceae	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 NPC881 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	460
0.1-0.2	1880
0.2-0.3	4077
0.3-0.4	8929
0.4-0.5	9016
0.5-0.6	4907
0.6-0.7	6096
0.7-0.8	5789
0.8-0.85	897
0.85-0.9	547
0.9-0.95	94
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 NPC881 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	399
0.1-0.2	1008
0.2-0.3	2123
0.3-0.4	2643
0.4-0.5	1806
0.5-0.6	776
0.6-0.7	269
0.7-0.8	104
0.8-0.85	13
0.85-0.9	9
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