NPASS Compound

Natural Product: NPC179285

Natural Product ID	NPC179285
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	LFEUICHQZGNOHD-SSCXBUAASA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	5538688
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0002506] Isoflavonoids [CHEMONTID:0000507] Isoflavonoid O-glycosides

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 54 57 0 0 0 0 0 0 0 0999 V2000 -9.7937 0.6702 -0.3904 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.8878 -0.2905 -0.8567 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.5214 -0.1274 -0.7106 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9698 0.9677 -0.1092 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.6138 1.0715 0.0052 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.7454 0.1045 -0.4660 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.3190 -1.0033 -1.0751 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.6844 -1.1340 -1.2041 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2963 0.2111 -0.3461 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6676 1.3843 -0.6429 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3553 1.5169 -0.5455 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.5803 0.5178 -0.1544 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7852 0.6686 -0.0569 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6198 -0.3531 0.3474 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0286 -1.5599 0.6586 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3470 -1.7261 0.5649 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1468 -0.6791 0.1564 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5134 -0.8535 0.0661 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0534 -1.9451 0.3471 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.9582 -2.9332 0.8741 O 0 0 0 0 0 0 0 0 0 0 0 0 2.9579 -0.1194 0.4163 O 0 0 0 0 0 0 0 0 0 0 0 0 3.9944 -0.9555 0.7846 C 0 0 2 0 0 0 0 0 0 0 0 0 4.7880 -0.4670 1.9715 C 0 0 2 0 0 0 0 0 0 0 0 0 5.2695 0.9292 1.6422 C 0 0 1 0 0 0 0 0 0 0 0 0 5.5293 1.0471 0.1592 C 0 0 2 0 0 0 0 0 0 0 0 0 5.9278 -0.3185 -0.3377 C 0 0 2 0 0 0 0 0 0 0 0 0 6.2943 -0.1526 -1.8159 C 0 0 0 0 0 0 0 0 0 0 0 0 7.3642 0.7125 -1.9833 O 0 0 0 0 0 0 0 0 0 0 0 0 4.8671 -1.1863 -0.2827 O 0 0 0 0 0 0 0 0 0 0 0 0 6.4920 2.0119 -0.1230 O 0 0 0 0 0 0 0 0 0 0 0 0 4.2159 1.8151 1.9338 O 0 0 0 0 0 0 0 0 0 0 0 0 5.8684 -1.3247 2.1708 O 0 0 0 0 0 0 0 0 0 0 0 0 -10.8272 0.2352 -0.3334 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.5291 0.9843 0.6404 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.8608 1.5242 -1.0802 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.6680 1.7317 0.2627 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.2061 1.9481 0.4851 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.6438 -1.7724 -1.4506 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.1065 -2.0090 -1.6838 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2325 2.2445 -0.9688 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1994 1.6316 -0.3114 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6136 -2.4093 0.9834 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0382 -3.2515 1.8158 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5860 -1.9529 1.0504 H 0 0 0 0 0 0 0 0 0 0 0 0 4.2073 -0.4640 2.9047 H 0 0 0 0 0 0 0 0 0 0 0 0 6.1231 1.2526 2.2488 H 0 0 0 0 0 0 0 0 0 0 0 0 4.6019 1.3454 -0.3622 H 0 0 0 0 0 0 0 0 0 0 0 0 6.8521 -0.6880 0.1505 H 0 0 0 0 0 0 0 0 0 0 0 0 6.5875 -1.1278 -2.2575 H 0 0 0 0 0 0 0 0 0 0 0 0 5.4496 0.2276 -2.4091 H 0 0 0 0 0 0 0 0 0 0 0 0 7.0674 1.5615 -2.3463 H 0 0 0 0 0 0 0 0 0 0 0 0 6.7755 2.5050 0.6789 H 0 0 0 0 0 0 0 0 0 0 0 0 3.8395 2.2313 1.1388 H 0 0 0 0 0 0 0 0 0 0 0 0 5.6606 -2.2472 1.8451 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 6 9 1 0 9 10 2 0 10 11 1 0 11 12 1 0 12 13 2 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 16 20 1 0 14 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 27 28 1 0 26 29 1 0 25 30 1 0 24 31 1 0 23 32 1 0 8 3 1 0 18 9 1 0 29 22 1 0 17 12 1 0 1 33 1 0 1 34 1 0 1 35 1 0 4 36 1 0 5 37 1 0 7 38 1 0 8 39 1 0 10 40 1 0 13 41 1 0 15 42 1 0 20 43 1 0 22 44 1 1 23 45 1 1 24 46 1 1 25 47 1 6 26 48 1 1 27 49 1 0 27 50 1 0 28 51 1 0 30 52 1 0 31 53 1 0 32 54 1 0 M END

Standard InCHIKey	LFEUICHQZGNOHD-SSCXBUAASA-N
Standard InCHI	InChI=1S/C22H22O10/c1-29-11-4-2-10(3-5-11)13-9-30-15-7-12(6-14(24)17(15)18(13)25)31-22-21(28)20(27)19(26)16(8-23)32-22/h2-7,9,16,19-24,26-28H,8H2,1H3/t16-,19-,20+,21-,22-/m0/s1
SMILES	COc1ccc(cc1)c1coc2cc(cc(c2c1=O)O)O[C@@H]1[C@H]([C@@H]([C@H]([C@H](CO)O1)O)O)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	446.12	Volume:	421.653 ? Van der Waals volume.
Dense:	1.058	LogP:	0.774 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	1.493 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-3.151 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	5.0	Rigid Bonds:	24.0
TPSA:	159.05 ? Topological Polar Surface Area.	H-Bond Acceptor:	10.0
H-Bond Donor:	5.0	Rings:	4.0
Heavy Atoms:	10.0

MedChem Properties

QED Drug-Likeness Score:	0.37	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	3.759	Fsp³:	0.318
MCE-18:	83.621 ? 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:	0.582	Fluc inhibitor:	0.517 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.886 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.738 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.105	Promiscuous compounds:	0.306

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-6.43	MDCK Permeability:	-5.348
Pgp-inhibitor:	0.005	Pgp-substrate:	0.317
PAMPA:	0.959 ? 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):	0.984
20% Bioavailability (F20%):	0.544	30% Bioavailability (F30%):	0.992
50% Bioavailability (F50%):	0.985

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.018	MRP1:	0.072
Plasma Protein Binding (PPB):	88.07%	Volume Distribution (VD):	-0.022
Fu:	12.166% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.994
OATP1B3 inhibitor:	0.999	BCRP inhibitor:	0.748
BSEP inhibitor:	0.036

ADMET: Metabolism

CYP1A2-inhibitor:	0.888	CYP1A2-substrate:	0.004
CYP2C19-inhibitor:	0.0	CYP2C19-substrate:	0.001
CYP2C9-inhibitor:	0.24	CYP2C9-substrate:	0.029
CYP2D6-inhibitor:	0.215	CYP2D6-substrate:	0.115
CYP3A4-inhibitor:	0.0	CYP3A4-substrate:	0.974
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.975
HLM stability:	0.01 ? 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):

2.183

Half-life (T1/2):

2.411

ADMET: Toxicity

hERG Blockers:	0.05	hERG Blockers (10um):	0.233
Human Hepatotoxicity (H-HT):	0.581	Drug-induced Liver Injury (DILI):	0.987
AMES Toxicity:	0.835	Rat Oral Acute Toxicity:	0.078
Maximum Recommended Daily Dose:	0.054	Skin Sensitization:	0.82
Carcinogencity:	0.183	Eye Corrosion:	0.0
Eye Irritation:	0.342	Respiratory Toxicity:	0.069
Drug-induced Neurotoxicity:	0.028	Ototoxicity:	0.812
Hematotoxicity:	0.17	Drug-induced Nephrotoxicity:	0.843
Genotoxicity:	0.507	RPMI-8226 Immunitoxicity:	0.192
A549 Cytotoxicity:	0.399	Hek293 Cytotoxicity:	0.187
BCF:	0.631 ? 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:	3.391 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	4.928 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.146 ? 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
NPO14039	Leucaena leucocephala	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO14039	Leucaena leucocephala	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO14039	Leucaena leucocephala	Species	Fabaceae	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 NPC179285 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	19707
0.1-0.2	25840
0.2-0.3	3010
0.3-0.4	933
0.4-0.5	269
0.5-0.6	58
0.6-0.7	25
0.7-0.8	0
0.8-0.85	3
0.85-0.9	0
0.9-0.95	1
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.9412	High Similarity	NPC73511
0.8451	Intermediate Similarity	NPC197896
0.8451	Intermediate Similarity	NPC313163
0.8194	Intermediate Similarity	NPC234739
0.7917	Intermediate Similarity	NPC160515
0.7467	Intermediate Similarity	NPC156457
0.7432	Intermediate Similarity	NPC45165
0.7403	Intermediate Similarity	NPC80140
0.72	Intermediate Similarity	NPC135345
0.716	Intermediate Similarity	NPC487212
0.7108	Intermediate Similarity	NPC479405
0.7105	Intermediate Similarity	NPC348541
0.7024	Intermediate Similarity	NPC479404
0.6835	Remote Similarity	NPC205076
0.6795	Remote Similarity	NPC95090
0.6795	Remote Similarity	NPC27408
0.679	Remote Similarity	NPC307518
0.6716	Remote Similarity	NPC116632
0.6667	Remote Similarity	NPC229729
0.6625	Remote Similarity	NPC100720
0.6625	Remote Similarity	NPC138540
0.6582	Remote Similarity	NPC487213
0.6582	Remote Similarity	NPC258035
0.6582	Remote Similarity	NPC161749
0.6543	Remote Similarity	NPC224462
0.6543	Remote Similarity	NPC479402
0.6375	Remote Similarity	NPC105511
0.6375	Remote Similarity	NPC603782
0.6341	Remote Similarity	NPC481043
0.631	Remote Similarity	NPC48773
0.6292	Remote Similarity	NPC479403
0.625	Remote Similarity	NPC289667
0.6145	Remote Similarity	NPC479401
0.6136	Remote Similarity	NPC303913
0.6118	Remote Similarity	NPC479407
0.6071	Remote Similarity	NPC22832
0.6071	Remote Similarity	NPC243930
0.6024	Remote Similarity	NPC60966
0.5904	Remote Similarity	NPC84362
0.5882	Remote Similarity	NPC486578
0.5882	Remote Similarity	NPC601607
0.5844	Remote Similarity	NPC133400
0.5814	Remote Similarity	NPC479406
0.5814	Remote Similarity	NPC607707
0.5769	Remote Similarity	NPC191154
0.5765	Remote Similarity	NPC285197
0.575	Remote Similarity	NPC25547
0.5698	Remote Similarity	NPC610187
0.5696	Remote Similarity	NPC134819
0.5694	Remote Similarity	NPC303644
0.5663	Remote Similarity	NPC39360
0.5663	Remote Similarity	NPC29763
0.5663	Remote Similarity	NPC210003
0.5641	Remote Similarity	NPC249824
0.5632	Remote Similarity	NPC311830
0.5595	Remote Similarity	NPC297987
0.5595	Remote Similarity	NPC277205
0.5595	Remote Similarity	NPC37919
0.5595	Remote Similarity	NPC136042
0.5595	Remote Similarity	NPC323593
0.5595	Remote Similarity	NPC203500
0.5595	Remote Similarity	NPC189142
0.5595	Remote Similarity	NPC77660
0.5529	Remote Similarity	NPC22195
0.5529	Remote Similarity	NPC186807
0.5529	Remote Similarity	NPC181712
0.5529	Remote Similarity	NPC21190
0.5476	Remote Similarity	NPC58053
0.5476	Remote Similarity	NPC261866
0.5476	Remote Similarity	NPC211014
0.5465	Remote Similarity	NPC472459
0.5455	Remote Similarity	NPC607201
0.5444	Remote Similarity	NPC251417
0.5402	Remote Similarity	NPC307938
0.5393	Remote Similarity	NPC267254
0.5393	Remote Similarity	NPC601586
0.5385	Remote Similarity	NPC203636
0.5341	Remote Similarity	NPC601144
0.5294	Remote Similarity	NPC259070
0.5281	Remote Similarity	NPC116458
0.5281	Remote Similarity	NPC246943
0.5281	Remote Similarity	NPC605784
0.527	Remote Similarity	NPC294409
0.527	Remote Similarity	NPC490701
0.5195	Remote Similarity	NPC114192
0.5158	Remote Similarity	NPC64425
0.5116	Remote Similarity	NPC44558
0.5116	Remote Similarity	NPC143851
0.5111	Remote Similarity	NPC220169
0.5106	Remote Similarity	NPC475155
0.5102	Remote Similarity	NPC475382
0.506	Remote Similarity	NPC488570
0.5057	Remote Similarity	NPC64305
0.5056	Remote Similarity	NPC611303
0.5053	Remote Similarity	NPC131745
0.5051	Remote Similarity	NPC235575

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC179285 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4666
0.1-0.2	4380
0.2-0.3	87
0.3-0.4	12
0.4-0.5	4
0.5-0.6	0
0.6-0.7	1
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
0.6582	Remote Similarity	NPD4381	Clinical (unspecified phase)

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