NPASS Compound

Natural Product: NPC480477

Natural Product ID	NPC480477
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	DWXCAOZAIWPIJR-PDSMFRHLSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	134151269
Chemical Classification	CHEMONTID:0000000 [Organic compounds]

The Chemical Classification was calculated by Classyfire, a software for chemical taxonomy calculation. Reference: DOI:10.1186/s13321-016-0174-y.

Chemical Representations

RDKit 3D 50 55 0 0 0 0 0 0 0 0999 V2000 -4.4729 0.1104 2.7578 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.6320 0.3726 1.3766 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.6337 0.1317 0.4552 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4248 -0.3786 0.8324 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3851 -0.6392 -0.0602 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6488 -0.3478 -1.3725 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8626 0.1675 -1.7709 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8660 0.4129 -0.8675 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9808 0.9308 -1.5379 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.5231 1.3406 -2.8050 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3688 0.5419 -3.0263 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.1155 -1.1882 0.4534 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8902 -0.1234 0.7490 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4100 1.0407 1.3414 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2965 2.0427 1.6386 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6310 1.9033 1.3584 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0937 0.7227 0.7613 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2133 -0.2877 0.4594 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6799 -1.5371 -0.1778 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5854 -1.8777 -1.1568 C 0 0 1 0 0 0 0 0 0 0 0 0 1.8057 -3.0998 -1.9825 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4467 -3.4661 -2.2793 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.4107 -2.9772 -1.2952 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6569 -3.0926 -1.3265 O 0 0 0 0 0 0 0 0 0 0 0 0 0.4314 -2.3414 -0.2859 C 0 0 2 0 0 0 0 0 0 0 0 0 4.4347 0.5602 0.4700 O 0 0 0 0 0 0 0 0 0 0 0 0 4.9781 0.9555 -0.7807 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3244 3.0493 1.7508 O 0 0 0 0 0 0 0 0 0 0 0 0 2.3263 4.0509 1.9888 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1269 3.2996 2.2211 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.6110 0.6791 3.1891 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.2887 -0.9845 2.8736 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.4327 0.3723 3.2553 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2675 -0.5917 1.8778 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9103 -0.5187 -2.1139 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.3285 1.1278 -3.5370 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.2510 2.4328 -2.8116 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3565 -1.5870 1.5007 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6571 1.1520 1.5654 H 0 0 0 0 0 0 0 0 0 0 0 0 2.7465 -2.3161 0.6265 H 0 0 0 0 0 0 0 0 0 0 0 0 3.6728 -1.4568 -0.6288 H 0 0 0 0 0 0 0 0 0 0 0 0 1.3736 -0.9732 -1.7197 H 0 0 0 0 0 0 0 0 0 0 0 0 2.2285 -3.8903 -1.3211 H 0 0 0 0 0 0 0 0 0 0 0 0 2.3858 -2.9403 -2.8997 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8134 -3.1585 0.3784 H 0 0 0 0 0 0 0 0 0 0 0 0 4.1770 1.0609 -1.5619 H 0 0 0 0 0 0 0 0 0 0 0 0 5.6513 0.1433 -1.1721 H 0 0 0 0 0 0 0 0 0 0 0 0 5.5954 1.8783 -0.6979 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5465 4.5561 2.9519 H 0 0 0 0 0 0 0 0 0 0 0 0 2.2201 4.7379 1.1434 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 3 4 2 0 4 5 1 0 5 6 2 0 6 7 1 0 7 8 2 0 8 9 1 0 9 10 1 0 10 11 1 0 5 12 1 0 12 13 1 0 13 14 2 0 14 15 1 0 15 16 2 0 16 17 1 0 17 18 2 0 18 19 1 0 19 20 1 0 20 21 1 0 21 22 1 0 22 23 1 0 23 24 2 0 23 25 1 0 17 26 1 0 26 27 1 0 16 28 1 0 28 29 1 0 29 30 1 0 8 3 1 0 25 12 1 0 11 7 1 0 18 13 1 0 25 20 1 0 30 15 1 0 1 31 1 0 1 32 1 0 1 33 1 0 4 34 1 0 6 35 1 0 10 36 1 0 10 37 1 0 12 38 1 1 14 39 1 0 19 40 1 0 19 41 1 0 20 42 1 6 21 43 1 0 21 44 1 0 25 45 1 1 27 46 1 0 27 47 1 0 27 48 1 0 29 49 1 0 29 50 1 0 M END

Standard InCHIKey	DWXCAOZAIWPIJR-PDSMFRHLSA-N
Standard InCHI	InChI=1S/C22H20O8/c1-24-14-4-10(5-15-20(14)29-8-27-15)17-12-6-16-21(30-9-28-16)19(25-2)13(12)3-11-7-26-22(23)18(11)17/h4-6,11,17-18H,3,7-9H2,1-2H3/t11-,17+,18-/m0/s1
SMILES	COc1cc(cc2c1OCO2)[C@@H]1c2cc3c(c(c2C[C@H]2COC(=O)[C@H]12)OC)OCO3

Calculated Properties

Physi-Chem Properties

Molecular Weight:	412.12	Volume:	389.596 ? Van der Waals volume.
Dense:	1.058	LogP:	2.216 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	2.408 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-4.504 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	3.0	Rigid Bonds:	30.0
TPSA:	81.68 ? Topological Polar Surface Area.	H-Bond Acceptor:	8.0
H-Bond Donor:	0.0	Rings:	6.0
Heavy Atoms:	8.0

MedChem Properties

QED Drug-Likeness Score:	0.712	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	3.905	Fsp³:	0.409
MCE-18:	107.0 ? MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.	Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Rejected	GSK Rule:	Accepted
Golden Triangle Rule:	Rejected	BMS Rule:	0
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.493	Fluc inhibitor:	0.314 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.464 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.075 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.222	Promiscuous compounds:	0.435

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-4.952	MDCK Permeability:	-4.744
Pgp-inhibitor:	0.176	Pgp-substrate:	0.002
PAMPA:	0.033 ? The experimental data for Peff was logarithmically transformed (logPeff). Molecules with log Peff values below 2.0 were classified as low-permeability (Category 0), while those with log Peff values exceeding 2.5 were classified as high-permeability (Category 1).	Human Intestinal Absorption (HIA):	0.0
20% Bioavailability (F20%):	0.001	30% Bioavailability (F30%):	0.0
50% Bioavailability (F50%):	0.013

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.998	MRP1:	0.963
Plasma Protein Binding (PPB):	97.5%	Volume Distribution (VD):	-0.004
Fu:	2.767% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.904
OATP1B3 inhibitor:	0.323	BCRP inhibitor:	0.0
BSEP inhibitor:	0.999

ADMET: Metabolism

CYP1A2-inhibitor:	0.998	CYP1A2-substrate:	0.83
CYP2C19-inhibitor:	1.0	CYP2C19-substrate:	0.821
CYP2C9-inhibitor:	0.0	CYP2C9-substrate:	0.519
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.993
CYP3A4-inhibitor:	1.0	CYP3A4-substrate:	1.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.0
HLM stability:	0.114 ? Human liver microsomal (HLM) stability. Category 0: stable+ (HLM > 30 min); Category 1: unstable- (HLM ≤ 30 min). The output value is the probability of human liver microsomal instability, where a value closer to 1 indicates a higher likelihood of instability.

ADMET: Excretion

Clearance (CL):

3.694

Half-life (T1/2):

1.632

ADMET: Toxicity

hERG Blockers:	0.203	hERG Blockers (10um):	0.577
Human Hepatotoxicity (H-HT):	0.934	Drug-induced Liver Injury (DILI):	0.998
AMES Toxicity:	0.849	Rat Oral Acute Toxicity:	0.907
Maximum Recommended Daily Dose:	0.874	Skin Sensitization:	0.989
Carcinogencity:	0.952	Eye Corrosion:	0.001
Eye Irritation:	0.389	Respiratory Toxicity:	0.971
Drug-induced Neurotoxicity:	0.957	Ototoxicity:	0.681
Hematotoxicity:	0.961	Drug-induced Nephrotoxicity:	0.986
Genotoxicity:	0.999	RPMI-8226 Immunitoxicity:	0.692
A549 Cytotoxicity:	0.893	Hek293 Cytotoxicity:	0.833
BCF:	1.673 ? Bioconcentration factors are used for considering secondary poisoning potential and assessing risks to human health via the food chain. The unit is -log10[(mg/L)/(1000*MW)].	IGC50:	4.094 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.878 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.904 ? 96 hour fathead minnow LC50. The unit of LC50FM is -log10[(mg/L)/(1000*MW)].

Species Source

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO8247	Austrobaileya scandens	Species	Austrobaileyaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[27214307]
NPO8247	Austrobaileya scandens	Species	Austrobaileyaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO8247	Austrobaileya scandens	Species	Austrobaileyaceae	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	Organism Name	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

Activity Type	# Activity
IC50	1

Activity Type	# Activity
Non-molecular	1

Molecular-level activity

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

In vitro activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT20529	Non-molecular	NON-PROTEIN TARGET	n.a.	IC50	=	47.0	nM	PMID[27214307]

In vivo activity

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

Experimental ADME

Experiment Model	Experiment Tissue	ADME Type	ADME Relation	ADME Value	ADME Unit	Reference

Experimental Toxicity

Quantitative toxicity

Experiment Model	Experiment Organism	Toxicity Type	Toxicity Relation	Toxicity Value	Toxicity Unit	Reference

Common Abbreviations:
LC: Lethal Concentration; LD: Lethal Dose; LT:Lethal Time; NOAEL: No-observed-adverse-effect Level; BMDL: Benchmark Dose Lower Confidence Limit; BMD: Benchmark Dose; BMC:Benchmark Concentration; LOAEL: Lowest Observed Adverse Effect Level; RfD:Reference Dose; RfC:Reference Concentration; MRL: Minimal Risk Level; MEG: Maximum Exposure Guideline; PAC: Protective Action Criteria

Categorical toxicity labels

Hepatotoxicity	Carcinogenicity	Mutagenicity	Cardiotoxicity	Respiratory Toxicity	Eye Irritation	Endocrine Disruption

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 toxicity records from domain-specific databases. These databases include:
☉ ToxValDB: a curated database that compiles quantitative toxicity values for chemicals from diverse public sources to support toxicological research and risk assessment.
☉ TOXRIC: a comprehensive, free-to-access, online database providing toxicological/feature data. The toxicity labels are retrieved from this database. [PMID: 36400569]

Chemically structural similarity

Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes approximately 50,000 NPs with experimentally-derived bioactivity available in NPASS)

Similarity is measured using the Tanimoto coefficient (Tc) , which compares the binary fingerprints of two molecules. Tc is calculated as the intersection divided by the union of '1' bits in the fingerprints, ranging from 0 to 1, with 1 indicating highest similarity.

● The left chart: Distribution of similarity level between NPC480477 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	28564
0.1-0.2	19920
0.2-0.3	1115
0.3-0.4	175
0.4-0.5	42
0.5-0.6	23
0.6-0.7	9
0.7-0.8	0
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
0.9623	High Similarity	NPC149505
0.7759	Intermediate Similarity	NPC262455
0.7759	Intermediate Similarity	NPC177476
0.7288	Intermediate Similarity	NPC80230
0.7288	Intermediate Similarity	NPC104024
0.7288	Intermediate Similarity	NPC101755
0.7288	Intermediate Similarity	NPC304687
0.7288	Intermediate Similarity	NPC65574
0.6667	Remote Similarity	NPC222531
0.6515	Remote Similarity	NPC115281
0.6061	Remote Similarity	NPC30009
0.6061	Remote Similarity	NPC207584
0.6061	Remote Similarity	NPC19947
0.6061	Remote Similarity	NPC103197
0.6032	Remote Similarity	NPC218092
0.6032	Remote Similarity	NPC246474
0.6032	Remote Similarity	NPC162851
0.5781	Remote Similarity	NPC239890
0.5781	Remote Similarity	NPC209411
0.5714	Remote Similarity	NPC163527
0.5667	Remote Similarity	NPC92693
0.5645	Remote Similarity	NPC164082
0.5593	Remote Similarity	NPC218841
0.5588	Remote Similarity	NPC210642
0.5588	Remote Similarity	NPC13985
0.5574	Remote Similarity	NPC40237
0.5556	Remote Similarity	NPC477698
0.5522	Remote Similarity	NPC237946
0.5522	Remote Similarity	NPC32373
0.55	Remote Similarity	NPC151423
0.5429	Remote Similarity	NPC273578
0.5375	Remote Similarity	NPC115624
0.5352	Remote Similarity	NPC288149
0.5352	Remote Similarity	NPC470637
0.5246	Remote Similarity	NPC193779
0.5211	Remote Similarity	NPC119910
0.5167	Remote Similarity	NPC11453
0.5161	Remote Similarity	NPC475000
0.5152	Remote Similarity	NPC191158
0.5152	Remote Similarity	NPC177644

Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

● The left chart: Distribution of similarity level between NPC480477 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	5435
0.1-0.2	3648
0.2-0.3	55
0.3-0.4	5
0.4-0.5	4
0.5-0.6	3
0.6-0.7	0
0.7-0.8	0
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
0.5522	Remote Similarity	NPD4965	Approved
0.5522	Remote Similarity	NPD4966	Phase 4
0.5522	Remote Similarity	NPD4967	Phase 2

Bioactivity similarity

Similar Natural Products in NPASS

Similarity level is defined by 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