NPASS Compound

Structure

NPC26314 OpenBabel06302215232D 40 43 0 0 1 0 0 0 0 0999 V2000 3.4270 -3.0657 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8337 -2.1521 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.2460 -1.3431 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2514 -1.4476 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6637 -0.6386 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0704 0.2749 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0649 0.3795 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6527 -0.4296 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6472 -0.3250 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.6691 -0.7431 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.1691 -1.6092 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.5759 -2.5227 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0119 -3.3317 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8090 -1.4013 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.6011 -2.3794 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3443 -3.0485 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2953 -2.7395 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0385 -3.4087 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5032 -1.7614 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7601 -1.0922 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4543 -1.4524 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.1974 -2.1215 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9135 -0.4067 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.7796 0.0933 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.7796 1.0933 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9135 1.5933 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.6456 -0.4067 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.5116 0.0933 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3776 -0.4067 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2437 0.0933 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2437 1.0933 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.1097 1.5933 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.1097 2.5933 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2437 3.0933 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2437 4.0933 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3776 1.5933 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5116 1.0933 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6456 1.5933 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.6456 2.5933 0.0000 C 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 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 6 7 2 0 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 10 5 1 6 0 0 0 10 11 1 0 0 0 0 10 40 1 0 0 0 0 11 12 1 1 0 0 0 11 14 1 0 0 0 0 12 13 1 0 0 0 0 14 20 1 1 0 0 0 14 15 1 0 0 0 0 14 23 1 0 0 0 0 15 16 2 0 0 0 0 16 17 1 0 0 0 0 17 18 2 0 0 0 0 17 19 1 0 0 0 0 19 20 2 0 0 0 0 19 21 1 0 0 0 0 21 22 1 0 0 0 0 23 24 1 1 0 0 0 23 40 1 0 0 0 0 24 25 1 1 0 0 0 24 27 1 0 0 0 0 25 26 1 0 0 0 0 27 28 1 0 0 0 0 28 37 2 0 0 0 0 28 29 1 0 0 0 0 29 30 2 0 0 0 0 30 31 1 0 0 0 0 31 32 1 0 0 0 0 31 36 2 0 0 0 0 32 33 1 0 0 0 0 33 34 1 0 0 0 0 34 35 1 0 0 0 0 36 37 1 0 0 0 0 37 38 1 0 0 0 0 38 39 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	448.21
Volume:	440.654
LogP:	2.023
LogD:	1.312
LogS:	-4.153
# Rotatable Bonds:	5
TPSA:	122.66
# H-Bond Aceptor:	8
# H-Bond Donor:	2
# Rings:	5
# Heavy Atoms:	8

MedChem Properties

QED Drug-Likeness Score:	0.286
Synthetic Accessibility Score:	5.8
Fsp3:	0.792
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.312
MDCK Permeability:	8.458332013105974e-05
Pgp-inhibitor:	0.041
Pgp-substrate:	0.997
Human Intestinal Absorption (HIA):	0.011
20% Bioavailability (F20%):	0.058
30% Bioavailability (F30%):	0.905

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.548
Plasma Protein Binding (PPB):	49.09984588623047%
Volume Distribution (VD):	0.751
Pgp-substrate:	69.35214233398438%

ADMET: Metabolism

CYP1A2-inhibitor:	0.01
CYP1A2-substrate:	0.973
CYP2C19-inhibitor:	0.015
CYP2C19-substrate:	0.754
CYP2C9-inhibitor:	0.007
CYP2C9-substrate:	0.019
CYP2D6-inhibitor:	0.003
CYP2D6-substrate:	0.104
CYP3A4-inhibitor:	0.417
CYP3A4-substrate:	0.387

ADMET: Excretion

Clearance (CL):	8.697
Half-life (T1/2):	0.219

ADMET: Toxicity

hERG Blockers:	0.231
Human Hepatotoxicity (H-HT):	0.967
Drug-inuced Liver Injury (DILI):	0.794
AMES Toxicity:	0.034
Rat Oral Acute Toxicity:	0.975
Maximum Recommended Daily Dose:	0.561
Skin Sensitization:	0.612
Carcinogencity:	0.85
Eye Corrosion:	0.008
Eye Irritation:	0.013
Respiratory Toxicity:	0.987

Download Data

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

Natural Product: NPC26314

Natural Product ID:	NPC26314
*Common Name:**	SZQZJNSCXOAEEV-QGFFCPEYSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	SZQZJNSCXOAEEV-QGFFCPEYSA-N
Standard InCHI:	InChI=1S/C30H36O10/c1-36-24-14-19(7-8-21(24)34)28-20(16-32)30(11-10-22(35)26(15-30)38-3)29(40-28)27(17-33)39-23-9-6-18(5-4-12-31)13-25(23)37-2/h6-11,13-15,20,27-29,31-34H,4-5,12,16-17H2,1-3H3/t20-,27+,28-,29-,30-/m1/s1
SMILES:	COc1cc(ccc1O)[C@@H]1[C@@H](CO)[C@]2(C=CC(=O)C(=C2)OC)[C@@H]([C@H](CO)Oc2ccc(CCCO)cc2OC)O1
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0002448] Benzenoids [CHEMONTID:0000134] Phenols [CHEMONTID:0000190] Methoxyphenols

*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
NPO6836	Alpinia blepharocalyx	Species	Zingiberaceae	Eukaryota	seeds	Mengha, Yunnan Province, China	1991-Aug	PMID[11277741]
NPO6836	Alpinia blepharocalyx	Species	Zingiberaceae	Eukaryota	seeds	n.a.	n.a.	PMID[11325233]
NPO6836	Alpinia blepharocalyx	Species	Zingiberaceae	Eukaryota	Seeds	n.a.	n.a.	PMID[11430002]
NPO3261	Aplysina archeri	Species	Aplysinidae	Eukaryota	n.a.	n.a.	n.a.	PMID[1324982]
NPO6457	Pinus strobus	Species	Pinaceae	Eukaryota	n.a.	heartwood	n.a.	PMID[13465274]
NPO17593	Pinus sylvestris	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[1536925]
NPO14054	Penicillium janczewskii	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[16180822]
NPO422	Euphorbia cornigera	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[17512094]
NPO422	Euphorbia cornigera	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19376614]
NPO17593	Pinus sylvestris	Species	Pinaceae	Eukaryota	n.a.	seed	n.a.	PMID[24225786]
NPO2697	Monodora tenuifolia	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[3509958]
NPO6836	Alpinia blepharocalyx	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[9461664]
NPO6836	Alpinia blepharocalyx	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO4564	Anguilla japonica	Species	Anguillidae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO17593	Pinus sylvestris	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO4564	Anguilla japonica	Species	Anguillidae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO17593	Pinus sylvestris	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO6836	Alpinia blepharocalyx	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO24089	Alcea rosea	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO2408	Millettia laurentii	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO17593	Pinus sylvestris	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO24089	Alcea rosea	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO8058	Pluchea odorata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2993	0totodarus sloanii	Species	Ommastrephidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1390	Melolontha melolontha	Species	Scarabaeidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6231	Cortinarius odoratus	Species	Cortinariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25760	Aspergillus striatus	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3956	Maesa ramentacea	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5584	Aldisa sanguinea	Species	Dorididae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7606	Salacia lehmbachii	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6836	Alpinia blepharocalyx	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7007	Eucalyptus jenseni	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1242	Balanops australiana	Species	Balanopaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5261	Sideroxylon cubense	Species	Sapotaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24089	Alcea rosea	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2250	Hylocomium splendens	Species	Hylocomiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO295	Kokoona reflexa	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3554	Aonidiella aurantii	Species	Diaspididae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3261	Aplysina archeri	Species	Aplysinidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4564	Anguilla japonica	Species	Anguillidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5975	Aspergillus carneus	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO422	Euphorbia cornigera	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7760	Macrolepiota neomastoidea	Species	Agaricaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18993	Araiostegiella perdurans	Species	Davalliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO849	Euonymus tingens	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6457	Pinus strobus	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2408	Millettia laurentii	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11747	Ocimum tenuiflorum	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4274	Alcyonium utinomii	Species	Alcyoniidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15487	Gymnopus confluens	Species	Omphalotaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2697	Monodora tenuifolia	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3408	Viguiera decurrens	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4949	Salvia yosgadensis	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3743	Sideritis brevibracteata	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17593	Pinus sylvestris	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1489	Pseudoplexaura flagellosa	Species	Plexauridae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7449	Eleutherobia albiflora	Species	Alcyoniidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14054	Penicillium janczewskii	Species	Aspergillaceae	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 NPC26314 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	379
0.1-0.2	1215
0.2-0.3	3020
0.3-0.4	7256
0.4-0.5	11348
0.5-0.6	4721
0.6-0.7	8760
0.7-0.8	5474
0.8-0.85	440
0.85-0.9	80
0.9-0.95	4
0.95-1	0

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 NPC26314 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	307
0.1-0.2	808
0.2-0.3	1671
0.3-0.4	2635
0.4-0.5	2020
0.5-0.6	1040
0.6-0.7	578
0.7-0.8	91
0.8-0.85	0
0.85-0.9	0
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