NPASS Compound

Natural Product: NPC604724

Natural Product ID	NPC604724
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	TXSJJCSJHIDTDE-JTVAWUQMSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL3793366
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 67 70 0 0 0 0 0 0 0 0999 V2000 -0.8151 4.7994 -0.9154 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2474 4.1852 -2.1178 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.3657 2.8163 -2.2572 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0814 1.9222 -1.2618 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2000 0.5424 -1.4003 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8685 -0.2941 -0.2312 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.0692 -0.8575 0.4172 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3379 -0.3430 0.0831 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.4625 -0.8687 0.6832 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.7430 -0.4051 0.3968 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3000 -1.8929 1.6008 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.4590 -2.4068 2.1937 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.3614 -3.4412 3.1276 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0765 -2.4008 1.9339 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9439 -1.8614 1.3205 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6077 -2.4032 1.6768 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5297 -1.9501 0.8300 C 0 0 1 0 0 0 0 0 0 0 0 0 1.4448 -3.1604 0.6470 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8882 -3.5840 1.8975 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0935 -1.4150 -0.5049 C 0 0 2 0 0 0 0 0 0 0 0 0 1.1725 -1.0974 -1.4814 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0191 -0.1055 -1.2618 O 0 0 0 0 0 0 0 0 0 0 0 0 2.9169 0.0126 -0.3006 C 0 0 2 0 0 0 0 0 0 0 0 0 2.5192 1.1124 0.5188 O 0 0 0 0 0 0 0 0 0 0 0 0 2.9800 2.3141 0.0369 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4215 2.4533 0.5482 C 0 0 1 0 0 0 0 0 0 0 0 0 4.4477 2.8904 1.8671 O 0 0 0 0 0 0 0 0 0 0 0 0 4.9949 1.0385 0.4358 C 0 0 2 0 0 0 0 0 0 0 0 0 6.3734 1.0611 0.3140 O 0 0 0 0 0 0 0 0 0 0 0 0 4.3203 0.3859 -0.7537 C 0 0 1 0 0 0 0 0 0 0 0 0 5.0609 -0.7838 -1.0239 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.6253 0.0868 -2.6057 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9217 0.9657 -3.6355 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7979 2.3299 -3.4791 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1001 3.2101 -4.5264 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.2887 4.2768 -0.0424 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2759 4.7441 -0.7908 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1218 5.8517 -0.8500 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7392 2.3298 -0.2981 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3696 0.3367 0.5560 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4235 0.4588 -0.6397 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.2373 -0.8030 -0.4080 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.9924 -3.0276 4.1039 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.3955 -3.8190 3.3442 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.7727 -4.3078 2.7892 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9478 -3.1986 2.6484 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6559 -3.5396 1.6830 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4000 -2.1515 2.7615 H 0 0 0 0 0 0 0 0 0 0 0 0 1.0405 -1.1347 1.4262 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7558 -3.9563 0.2323 H 0 0 0 0 0 0 0 0 0 0 0 0 2.2705 -2.9805 -0.0438 H 0 0 0 0 0 0 0 0 0 0 0 0 1.7774 -2.8915 2.5993 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5625 -2.2563 -0.9324 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6219 -0.8536 -2.4542 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6505 -2.0847 -1.7511 H 0 0 0 0 0 0 0 0 0 0 0 0 3.0641 -0.8005 0.4335 H 0 0 0 0 0 0 0 0 0 0 0 0 2.9112 2.4452 -1.0449 H 0 0 0 0 0 0 0 0 0 0 0 0 2.4079 3.1179 0.5304 H 0 0 0 0 0 0 0 0 0 0 0 0 4.9761 3.1419 -0.0957 H 0 0 0 0 0 0 0 0 0 0 0 0 3.7470 2.4600 2.4203 H 0 0 0 0 0 0 0 0 0 0 0 0 4.7226 0.4315 1.3270 H 0 0 0 0 0 0 0 0 0 0 0 0 6.6656 1.9699 0.6227 H 0 0 0 0 0 0 0 0 0 0 0 0 4.3420 1.0955 -1.5779 H 0 0 0 0 0 0 0 0 0 0 0 0 4.7789 -1.1163 -1.9276 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7325 -0.9915 -2.7431 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2596 0.5900 -4.5914 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9072 3.8078 -4.5212 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 2 0 8 9 1 0 9 10 1 0 9 11 2 0 11 12 1 0 12 13 1 0 11 14 1 0 14 15 2 0 15 16 1 0 16 17 1 0 17 18 1 0 18 19 1 0 17 20 1 0 20 21 1 0 21 22 1 0 22 23 1 0 23 24 1 0 24 25 1 0 25 26 1 0 26 27 1 0 26 28 1 0 28 29 1 0 28 30 1 0 30 31 1 0 5 32 2 0 32 33 1 0 33 34 2 0 34 35 1 0 34 3 1 0 20 6 1 0 30 23 1 0 15 7 1 0 1 36 1 0 1 37 1 0 1 38 1 0 4 39 1 0 6 40 1 1 8 41 1 0 10 42 1 0 13 43 1 0 13 44 1 0 13 45 1 0 14 46 1 0 16 47 1 0 16 48 1 0 17 49 1 1 18 50 1 0 18 51 1 0 19 52 1 0 20 53 1 6 21 54 1 0 21 55 1 0 23 56 1 1 25 57 1 0 25 58 1 0 26 59 1 6 27 60 1 0 28 61 1 1 29 62 1 0 30 63 1 6 31 64 1 0 32 65 1 0 33 66 1 0 35 67 1 0 M END

Standard InCHIKey	TXSJJCSJHIDTDE-JTVAWUQMSA-N
Standard InCHI	InChI=1S/C25H32O10/c1-32-20-6-12(3-4-17(20)27)22-15-8-18(28)21(33-2)7-13(15)5-14(9-26)16(22)10-34-25-24(31)23(30)19(29)11-35-25/h3-4,6-8,14,16,19,22-31H,5,9-11H2,1-2H3/t14-,16-,19+,22-,23-,24+,25+/m0/s1
SMILES	COc1cc([C@H]2c3cc(O)c(OC)cc3C[C@@H](CO)[C@@H]2CO[C@@H]2OC[C@@H](O)[C@H](O)[C@H]2O)ccc1O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	492.2	Volume:	478.814 ? Van der Waals volume.
Dense:	1.028	LogP:	0.899 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	1.433 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-3.006 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	7.0	Rigid Bonds:	23.0
TPSA:	158.3 ? Topological Polar Surface Area.	H-Bond Acceptor:	10.0
H-Bond Donor:	6.0	Rings:	4.0
Heavy Atoms:	10.0

MedChem Properties

QED Drug-Likeness Score:	0.321	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	4.381	Fsp³:	0.52
MCE-18:	90.316 ? 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:	1	PAINS Alert:	0
Colloidal aggregators:	0.516	Fluc inhibitor:	0.317 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.195 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.051 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.073	Promiscuous compounds:	0.136

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-6.34	MDCK Permeability:	-5.38
Pgp-inhibitor:	0.0	Pgp-substrate:	0.818
PAMPA:	0.459 ? 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):	0.008
20% Bioavailability (F20%):	0.593	30% Bioavailability (F30%):	0.974
50% Bioavailability (F50%):	0.998

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.003	MRP1:	0.76
Plasma Protein Binding (PPB):	69.643%	Volume Distribution (VD):	-0.315
Fu:	30.27% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	1.0
OATP1B3 inhibitor:	1.0	BCRP inhibitor:	0.163
BSEP inhibitor:	0.017

ADMET: Metabolism

CYP1A2-inhibitor:	0.001	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	1.0	CYP2C19-substrate:	0.001
CYP2C9-inhibitor:	0.003	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.012
CYP3A4-inhibitor:	0.999	CYP3A4-substrate:	1.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	1.0
HLM stability:	0.005 ? 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):

2.538

Half-life (T1/2):

2.643

ADMET: Toxicity

hERG Blockers:	0.07	hERG Blockers (10um):	0.227
Human Hepatotoxicity (H-HT):	0.765	Drug-induced Liver Injury (DILI):	0.14
AMES Toxicity:	0.657	Rat Oral Acute Toxicity:	0.045
Maximum Recommended Daily Dose:	0.217	Skin Sensitization:	0.99
Carcinogencity:	0.141	Eye Corrosion:	0.0
Eye Irritation:	0.335	Respiratory Toxicity:	0.061
Drug-induced Neurotoxicity:	0.075	Ototoxicity:	0.931
Hematotoxicity:	0.144	Drug-induced Nephrotoxicity:	0.815
Genotoxicity:	0.074	RPMI-8226 Immunitoxicity:	0.146
A549 Cytotoxicity:	0.55	Hek293 Cytotoxicity:	0.589
BCF:	0.623 ? 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:	3.141 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	4.724 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	3.794 ? 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
NPO5852	Litsea glutinosa	Species	Lauraceae	Eukaryota	n.a.	stem	n.a.	DOI[10.1016/S0031-9422(00)88469-1]
NPO5852	Litsea glutinosa	Species	Lauraceae	Eukaryota	n.a.	leaf	n.a.	DOI[10.1016/S0031-9422(00)88469-1]
NPO5852	Litsea glutinosa	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO12328	Ampelopsis japonica	Species	Vitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO12328	Ampelopsis japonica	Species	Vitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO5852	Litsea glutinosa	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO12328	Ampelopsis japonica	Species	Vitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO5852	Litsea glutinosa	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12328	Ampelopsis japonica	Species	Vitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO5852	Litsea glutinosa	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12328	Ampelopsis japonica	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	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
Individual protein	1

Molecular-level activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT1464	Individual protein	Phosphodiesterase 4D	Homo sapiens	IC50	>	20000.0	nM	PMID[26978121]

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 NPC604724 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	19633
0.1-0.2	27002
0.2-0.3	2888
0.3-0.4	295
0.4-0.5	18
0.5-0.6	13
0.6-0.7	6
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
1.0	High Similarity	NPC471065
0.7917	Intermediate Similarity	NPC272619
0.7808	Intermediate Similarity	NPC286245
0.6849	Remote Similarity	NPC182368
0.6849	Remote Similarity	NPC606312
0.6197	Remote Similarity	NPC172230
0.6197	Remote Similarity	NPC278808
0.6119	Remote Similarity	NPC277458
0.6119	Remote Similarity	NPC307050
0.5753	Remote Similarity	NPC29599
0.5432	Remote Similarity	NPC185955
0.5432	Remote Similarity	NPC9933
0.5432	Remote Similarity	NPC145979
0.5432	Remote Similarity	NPC469706
0.5432	Remote Similarity	NPC218041
0.5432	Remote Similarity	NPC214326
0.5432	Remote Similarity	NPC260781
0.5366	Remote Similarity	NPC225815
0.5366	Remote Similarity	NPC602887
0.5143	Remote Similarity	NPC266705
0.5143	Remote Similarity	NPC29008
0.5068	Remote Similarity	NPC311256

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC604724 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4791
0.1-0.2	4274
0.2-0.3	84
0.3-0.4	1
0.4-0.5	0
0.5-0.6	0
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
		NPD

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