NPASS Compound

Natural Product: NPC574923

Natural Product ID	NPC574923
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	desoxypodophyllotoxin
IUPAC Name	5-(3,4,5-trimethoxyphenyl)-8,9-dihydroisobenzofuro[6,5-f][1,3]benzodioxol-6-one
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	n.a.
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 48 52 0 0 0 0 0 0 0 0999 V2000 2.8439 3.5870 0.8631 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3867 2.4333 0.2327 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5919 1.2911 0.1441 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3051 1.2493 0.6465 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5164 0.1179 0.5594 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8339 0.1582 1.1165 C 0 0 0 0 0 3 0 0 0 0 0 0 -1.2910 -1.0534 1.8092 C 0 0 0 0 0 3 0 0 0 0 0 0 -1.7289 -2.1658 0.8429 C 0 0 0 0 0 3 0 0 0 0 0 0 -1.8838 -3.2949 1.8399 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7271 -3.1054 2.6512 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.3545 -1.7692 2.6493 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6324 -1.3298 3.2869 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.0059 -1.7112 0.2275 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8649 -0.3151 -0.2891 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8194 0.0762 -1.2263 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7888 1.3449 -1.7739 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8011 2.2082 -1.3760 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8621 1.8045 -0.4456 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8676 0.5463 0.1173 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0277 3.3938 -2.0911 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3430 3.3613 -2.6468 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.6223 1.9586 -2.7148 O 0 0 0 0 0 0 0 0 0 0 0 0 1.0806 -0.9794 -0.0595 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3599 -0.9767 -0.5728 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9050 -2.0926 -1.1905 O 0 0 0 0 0 0 0 0 0 0 0 0 2.1233 -3.2671 -1.2959 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1212 0.1592 -0.4730 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4211 0.2000 -0.9810 O 0 0 0 0 0 0 0 0 0 0 0 0 5.5496 -0.1526 -0.2080 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6607 3.3326 1.9308 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5825 4.3887 0.7935 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8925 3.8504 0.3442 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9436 2.1546 1.1152 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7768 -3.1506 2.5004 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8662 -4.2889 1.3745 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3192 -2.3836 -0.5995 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.7984 -1.6961 0.9936 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.6089 -0.5958 -1.5525 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1076 2.5099 -0.1623 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.0825 3.8346 -2.0013 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3541 3.7255 -3.6860 H 0 0 0 0 0 0 0 0 0 0 0 0 0.5092 -1.8681 -0.1472 H 0 0 0 0 0 0 0 0 0 0 0 0 1.2559 -3.0095 -1.9400 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8091 -3.5438 -0.2614 H 0 0 0 0 0 0 0 0 0 0 0 0 2.7115 -4.0926 -1.7449 H 0 0 0 0 0 0 0 0 0 0 0 0 6.0560 0.7131 0.2396 H 0 0 0 0 0 0 0 0 0 0 0 0 5.2163 -0.8883 0.5569 H 0 0 0 0 0 0 0 0 0 0 0 0 6.2615 -0.6686 -0.8915 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 1 0 6 7 1 0 7 8 1 0 8 9 1 0 9 10 1 0 10 11 1 0 11 12 2 0 8 13 1 0 13 14 1 0 14 15 2 0 15 16 1 0 16 17 2 0 17 18 1 0 18 19 2 0 17 20 1 0 20 21 1 0 21 22 1 0 5 23 2 0 23 24 1 0 24 25 1 0 25 26 1 0 24 27 2 0 27 28 1 0 28 29 1 0 27 3 1 0 19 6 1 0 11 7 1 0 19 14 1 0 22 16 1 0 1 30 1 0 1 31 1 0 1 32 1 0 4 33 1 0 9 34 1 0 9 35 1 0 13 36 1 0 13 37 1 0 15 38 1 0 18 39 1 0 21 40 1 0 21 41 1 0 23 42 1 0 26 43 1 0 26 44 1 0 26 45 1 0 29 46 1 0 29 47 1 0 29 48 1 0 M RAD 3 6 2 7 2 8 2 M END

Standard InCHIKey	RSQHYDRYCKDMRM-UHFFFAOYSA-N
Standard InCHI	InChI=1S/C22H19O7/c1-24-17-6-12(7-18(25-2)21(17)26-3)19-14-8-16-15(28-10-29-16)5-11(14)4-13-9-27-22(23)20(13)19/h5-8H,4,9-10H2,1-3H3
SMILES	COC1=CC([C]2[C]3[C](COC3=O)CC3=CC4=C(C=C23)OCO4)=CC(OC)=C1OC

Calculated Properties

Physi-Chem Properties

Molecular Weight:	395.11	Volume:	385.408 ? Van der Waals volume.
Dense:	1.025	LogP:	2.545 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	2.674 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-4.966 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	4.0	Rigid Bonds:	26.0
TPSA:	72.45 ? Topological Polar Surface Area.	H-Bond Acceptor:	7.0
H-Bond Donor:	0.0	Rings:	5.0
Heavy Atoms:	7.0

MedChem Properties

QED Drug-Likeness Score:	0.737	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	3.184	Fsp³:	0.273
MCE-18:	59.786 ? 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:	Rejected
Golden Triangle Rule:	Rejected	BMS Rule:	0
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.25	Fluc inhibitor:	0.004 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.565 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.172 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.247	Promiscuous compounds:	0.215

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-4.705	MDCK Permeability:	-4.654
Pgp-inhibitor:	0.045	Pgp-substrate:	0.002
PAMPA:	0.114 ? 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%):	0.011	30% Bioavailability (F30%):	0.0
50% Bioavailability (F50%):	0.161

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.99	MRP1:	0.998
Plasma Protein Binding (PPB):	98.233%	Volume Distribution (VD):	-0.145
Fu:	1.584% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.718
OATP1B3 inhibitor:	0.917	BCRP inhibitor:	0.002
BSEP inhibitor:	1.0

ADMET: Metabolism

CYP1A2-inhibitor:	0.882	CYP1A2-substrate:	0.972
CYP2C19-inhibitor:	1.0	CYP2C19-substrate:	0.813
CYP2C9-inhibitor:	0.996	CYP2C9-substrate:	0.718
CYP2D6-inhibitor:	0.947	CYP2D6-substrate:	1.0
CYP3A4-inhibitor:	0.988	CYP3A4-substrate:	1.0
CYP2B6-substrate:	0.989	CYP2C8-inhibitor:	0.001
HLM stability:	0.656 ? 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):

3.221

Half-life (T1/2):

1.31

ADMET: Toxicity

hERG Blockers:	0.17	hERG Blockers (10um):	0.474
Human Hepatotoxicity (H-HT):	0.818	Drug-induced Liver Injury (DILI):	0.889
AMES Toxicity:	0.773	Rat Oral Acute Toxicity:	0.46
Maximum Recommended Daily Dose:	0.837	Skin Sensitization:	0.913
Carcinogencity:	0.964	Eye Corrosion:	0.001
Eye Irritation:	0.328	Respiratory Toxicity:	0.36
Drug-induced Neurotoxicity:	0.793	Ototoxicity:	0.506
Hematotoxicity:	0.841	Drug-induced Nephrotoxicity:	0.917
Genotoxicity:	0.898	RPMI-8226 Immunitoxicity:	0.39
A549 Cytotoxicity:	0.316	Hek293 Cytotoxicity:	0.468
BCF:	1.559 ? 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:	4.13 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.96 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	5.075 ? 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
NPO12785	Bursera fagaroides	Species	Burseraceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO12785	Bursera fagaroides	Species	Burseraceae	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

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

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 NPC574923 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	28526
0.1-0.2	19671
0.2-0.3	1365
0.3-0.4	197
0.4-0.5	52
0.5-0.6	20
0.6-0.7	8
0.7-0.8	0
0.8-0.85	3
0.85-0.9	0
0.9-0.95	2
0.95-1	5

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC80230
1.0	High Similarity	NPC104024
1.0	High Similarity	NPC101755
1.0	High Similarity	NPC304687
1.0	High Similarity	NPC65574
0.9423	High Similarity	NPC262455
0.9423	High Similarity	NPC177476
0.8	Intermediate Similarity	NPC218092
0.8	Intermediate Similarity	NPC246474
0.8	Intermediate Similarity	NPC162851
0.7931	Intermediate Similarity	NPC30009
0.7931	Intermediate Similarity	NPC103197
0.7586	Intermediate Similarity	NPC149505
0.7288	Intermediate Similarity	NPC480477
0.6984	Remote Similarity	NPC115281
0.6806	Remote Similarity	NPC115624
0.65	Remote Similarity	NPC239890
0.65	Remote Similarity	NPC209411
0.619	Remote Similarity	NPC237946
0.619	Remote Similarity	NPC32373
0.6	Remote Similarity	NPC210642
0.6	Remote Similarity	NPC13985
0.5965	Remote Similarity	NPC480480
0.5882	Remote Similarity	NPC163527
0.5763	Remote Similarity	NPC23336
0.5758	Remote Similarity	NPC207584
0.5758	Remote Similarity	NPC19947
0.5588	Remote Similarity	NPC119910
0.557	Remote Similarity	NPC222531
0.55	Remote Similarity	NPC40237
0.5484	Remote Similarity	NPC477698
0.5424	Remote Similarity	NPC151423
0.5397	Remote Similarity	NPC176586
0.5397	Remote Similarity	NPC210354
0.5333	Remote Similarity	NPC92693
0.5323	Remote Similarity	NPC164082
0.5254	Remote Similarity	NPC218841
0.5082	Remote Similarity	NPC475000
0.5077	Remote Similarity	NPC191158
0.5077	Remote Similarity	NPC177644
0.507	Remote Similarity	NPC288149
0.507	Remote Similarity	NPC470637

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC574923 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	5426
0.1-0.2	3621
0.2-0.3	90
0.3-0.4	6
0.4-0.5	4
0.5-0.6	0
0.6-0.7	3
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
0.619	Remote Similarity	NPD4965	Approved
0.619	Remote Similarity	NPD4966	Phase 4
0.619	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