NPASS Compound

Natural Product: NPC472269

Natural Product ID	NPC472269
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	JZWICBROGGTPEB-BVTFHXJVSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL3357151
PubChem CID	n.a.
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0002049] Terpene glycosides [CHEMONTID:0001580] Triterpene glycosides [CHEMONTID:0002358] Triterpene saponins

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

Chemical Representations

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81206 1 0 82207 1 0 82208 1 0 82209 1 0 83210 1 0 83211 1 0 83212 1 0 84213 1 0 84214 1 0 85215 1 0 85216 1 0 86217 1 6 88218 1 0 88219 1 0 88220 1 0 89221 1 0 89222 1 0 90223 1 0 90224 1 0 91225 1 6 93226 1 0 93227 1 0 93228 1 0 94229 1 0 94230 1 0 94231 1 0 96232 1 6 98233 1 6 99234 1 0 99235 1 0 101236 1 1 103237 1 0 103238 1 0 104239 1 1 105240 1 1 106241 1 6 108242 1 1 110243 1 0 110244 1 0 111245 1 6 112246 1 1 113247 1 6 114248 1 0 115249 1 0 116250 1 0 117251 1 0 118252 1 0 119253 1 1 120254 1 6 121255 1 1 122256 1 0 123257 1 0 124258 1 0 125259 1 0 125260 1 0 125261 1 0 126262 1 0 126263 1 0 126264 1 0 M END

Standard InCHIKey	JZWICBROGGTPEB-BVTFHXJVSA-N
Standard InCHI	InChI=1S/C88H138O38/c1-14-83(9,109)24-16-18-40(3)71(106)111-38-50-58(98)68(121-72(107)42(33-89)19-17-25-84(10,110)15-2)70(125-76-64(104)60(100)66(41(4)117-76)122-75-65(105)67(48(93)37-114-75)123-73-61(101)54(94)45(90)34-112-73)79(119-50)126-80(108)88-30-28-81(5,6)32-44(88)43-20-21-52-85(11)26-23-53(82(7,8)51(85)22-27-87(52,13)86(43,12)29-31-88)120-77-63(103)59(99)57(97)49(118-77)39-116-78-69(56(96)47(92)36-115-78)124-74-62(102)55(95)46(91)35-113-74/h14-15,18-20,41,44-70,73-79,89-105,109-110H,1-2,16-17,21-39H2,3-13H3/b40-18+,42-19-/t41-,44-,45+,46+,47-,48+,49+,50+,51-,52+,53-,54-,55-,56-,57+,58+,59-,60-,61+,62+,63+,64+,65+,66-,67-,68-,69+,70+,73-,74-,75-,76-,77-,78-,79-,83+,84?,85-,86+,87+,88-/m0/s1
SMILES	OC/C(=C/CCC(C=C)(O)C)/C(=O)O[C@@H]1[C@@H](O[C@@H]2O[C@@H](C)[C@@H]([C@H]([C@H]2O)O)O[C@@H]2OC[C@H]([C@@H]([C@H]2O)O[C@@H]2OC[C@H]([C@@H]([C@H]2O)O)O)O)[C@@H](O[C@@H]([C@H]1O)COC(=O)/C(=C/CC[C@@](C=C)(O)C)/C)OC(=O)[C@@]12CCC(C[C@H]2C2=CC[C@H]3[C@@]([C@@]2(CC1)C)(C)CC[C@@H]1[C@]3(C)CC[C@@H](C1(C)C)O[C@@H]1O[C@H](CO[C@@H]2OC[C@@H]([C@@H]([C@H]2O[C@@H]2OC[C@H]([C@@H]([C@H]2O)O)O)O)O)[C@H]([C@@H]([C@H]1O)O)O)(C)C

Calculated Properties

Physi-Chem Properties

Molecular Weight:	1802.89	Volume:	1740.863 ? Van der Waals volume.
Dense:	1.036	LogP:	1.31 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	1.838 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-3.71 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	32.0	Rigid Bonds:	75.0
TPSA:	583.26 ? Topological Polar Surface Area.	H-Bond Acceptor:	38.0
H-Bond Donor:	19.0	Rings:	12.0
Heavy Atoms:	38.0

MedChem Properties

QED Drug-Likeness Score:	0.013	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	8.161	Fsp³:	0.852
MCE-18:	270.16 ? MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.	Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected	GSK Rule:	Accepted
Golden Triangle Rule:	Accepted	BMS Rule:	1
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.876	Fluc inhibitor:	0.003 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.0 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.008 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.37	Promiscuous compounds:	0.591

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-6.354	MDCK Permeability:	-5.104
Pgp-inhibitor:	0.0	Pgp-substrate:	0.858
PAMPA:	1.0 ? 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):	0.12
20% Bioavailability (F20%):	0.988	30% Bioavailability (F30%):	1.0
50% Bioavailability (F50%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.0	MRP1:	0.0
Plasma Protein Binding (PPB):	54.473%	Volume Distribution (VD):	-0.395
Fu:	19.134% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	1.0
OATP1B3 inhibitor:	1.0	BCRP inhibitor:	0.003
BSEP inhibitor:	0.0

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.0	CYP2C19-substrate:	0.0
CYP2C9-inhibitor:	0.0	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.005
CYP3A4-inhibitor:	0.001	CYP3A4-substrate:	0.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.997
HLM stability:	0.086 ? 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):

-1.234

Half-life (T1/2):

4.133

ADMET: Toxicity

hERG Blockers:	0.0	hERG Blockers (10um):	0.001
Human Hepatotoxicity (H-HT):	0.382	Drug-induced Liver Injury (DILI):	0.113
AMES Toxicity:	0.903	Rat Oral Acute Toxicity:	0.0
Maximum Recommended Daily Dose:	0.0	Skin Sensitization:	1.0
Carcinogencity:	0.002	Eye Corrosion:	0.0
Eye Irritation:	0.0	Respiratory Toxicity:	0.0
Drug-induced Neurotoxicity:	0.0	Ototoxicity:	1.0
Hematotoxicity:	0.17	Drug-induced Nephrotoxicity:	0.999
Genotoxicity:	0.005	RPMI-8226 Immunitoxicity:	0.424
A549 Cytotoxicity:	0.877	Hek293 Cytotoxicity:	0.605
BCF:	0.057 ? 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:	3.735 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	6.146 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.751 ? 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
NPO20608	Gleditsia sinensis	Species	Fabaceae	Eukaryota	anomalous fruits	n.a.	n.a.	PMID[25442304]
NPO20608	Gleditsia sinensis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO20608	Gleditsia sinensis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO20608	Gleditsia sinensis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO20608	Gleditsia sinensis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO20608	Gleditsia sinensis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO20608	Gleditsia sinensis	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

Activity Type	# Activity
Activity	2
IC50	2

Activity Type	# Activity
Cell line	4

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
NPT380	Cell line	U-251	Homo sapiens	Activity	=	9.84	%	PMID[25442304]
NPT76	Cell line	C6	Rattus norvegicus	Activity	=	10.25	%	DrugMatrix in vivo data: Hematology
NPT380	Cell line	U-251	Homo sapiens	IC50	=	15180.0	nM	PMID[25442304]
NPT76	Cell line	C6	Rattus norvegicus	IC50	=	13630.0	nM	DOI[10.6019/CHEMBL1201861]

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 NPC472269 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	26393
0.1-0.2	20736
0.2-0.3	1910
0.3-0.4	478
0.4-0.5	218
0.5-0.6	100
0.6-0.7	12
0.7-0.8	0
0.8-0.85	0
0.85-0.9	2
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.8841	High Similarity	NPC472268
0.8768	High Similarity	NPC297950
0.7895	Intermediate Similarity	NPC472270
0.7895	Intermediate Similarity	NPC112492
0.7355	Intermediate Similarity	NPC23020
0.7324	Intermediate Similarity	NPC70809
0.7273	Intermediate Similarity	NPC224381
0.6621	Remote Similarity	NPC13998
0.66	Remote Similarity	NPC102505
0.66	Remote Similarity	NPC488514
0.6405	Remote Similarity	NPC480422
0.6301	Remote Similarity	NPC488560
0.6259	Remote Similarity	NPC85154
0.6225	Remote Similarity	NPC309223
0.6194	Remote Similarity	NPC8524
0.6159	Remote Similarity	NPC236638
0.6159	Remote Similarity	NPC294453
0.6154	Remote Similarity	NPC33012
0.6053	Remote Similarity	NPC481081
0.5977	Remote Similarity	NPC488200
0.5921	Remote Similarity	NPC41061
0.5921	Remote Similarity	NPC227551
0.5906	Remote Similarity	NPC475160
0.5906	Remote Similarity	NPC473714
0.5897	Remote Similarity	NPC250247
0.5894	Remote Similarity	NPC57484
0.5844	Remote Similarity	NPC305981
0.5839	Remote Similarity	NPC123199
0.5829	Remote Similarity	NPC488203
0.5828	Remote Similarity	NPC481080
0.5819	Remote Similarity	NPC475527
0.5806	Remote Similarity	NPC261506
0.5806	Remote Similarity	NPC4328
0.5789	Remote Similarity	NPC476068
0.5743	Remote Similarity	NPC60557
0.5743	Remote Similarity	NPC67857
0.5742	Remote Similarity	NPC202828
0.5742	Remote Similarity	NPC119592
0.5706	Remote Similarity	NPC488204
0.5705	Remote Similarity	NPC79643
0.5697	Remote Similarity	NPC484830
0.5685	Remote Similarity	NPC295823
0.5685	Remote Similarity	NPC174720
0.5685	Remote Similarity	NPC475467
0.5646	Remote Similarity	NPC104137
0.5646	Remote Similarity	NPC26626
0.5629	Remote Similarity	NPC135904
0.5629	Remote Similarity	NPC480419
0.5618	Remote Similarity	NPC488202
0.5577	Remote Similarity	NPC43550
0.5562	Remote Similarity	NPC475599
0.5556	Remote Similarity	NPC63159
0.5548	Remote Similarity	NPC480418
0.5541	Remote Similarity	NPC481078
0.551	Remote Similarity	NPC481079
0.55	Remote Similarity	NPC488201
0.5466	Remote Similarity	NPC480417
0.5461	Remote Similarity	NPC173583
0.5449	Remote Similarity	NPC286457
0.5434	Remote Similarity	NPC485563
0.543	Remote Similarity	NPC475287
0.5422	Remote Similarity	NPC475177
0.5409	Remote Similarity	NPC298034
0.5409	Remote Similarity	NPC71065
0.5393	Remote Similarity	NPC322904
0.539	Remote Similarity	NPC475516
0.538	Remote Similarity	NPC293330
0.5379	Remote Similarity	NPC488526
0.5371	Remote Similarity	NPC475444
0.5371	Remote Similarity	NPC473679
0.5361	Remote Similarity	NPC475368
0.5357	Remote Similarity	NPC475345
0.535	Remote Similarity	NPC110633
0.5342	Remote Similarity	NPC220160
0.5329	Remote Similarity	NPC76972
0.5329	Remote Similarity	NPC469782
0.5329	Remote Similarity	NPC204414
0.5322	Remote Similarity	NPC45606
0.5294	Remote Similarity	NPC187497
0.5287	Remote Similarity	NPC473386
0.5267	Remote Similarity	NPC241909
0.526	Remote Similarity	NPC475584
0.526	Remote Similarity	NPC475152
0.5256	Remote Similarity	NPC471577
0.5241	Remote Similarity	NPC480421
0.522	Remote Similarity	NPC475514
0.5217	Remote Similarity	NPC144644
0.5217	Remote Similarity	NPC37860
0.5217	Remote Similarity	NPC170407
0.5206	Remote Similarity	NPC475649
0.5193	Remote Similarity	NPC324933
0.5188	Remote Similarity	NPC65105
0.5183	Remote Similarity	NPC68767
0.5183	Remote Similarity	NPC293031
0.5169	Remote Similarity	NPC469776
0.5161	Remote Similarity	NPC174336
0.5161	Remote Similarity	NPC165204
0.5155	Remote Similarity	NPC136768
0.5148	Remote Similarity	NPC489208
0.5141	Remote Similarity	NPC48499
0.5132	Remote Similarity	NPC187290
0.5115	Remote Similarity	NPC220838
0.5096	Remote Similarity	NPC100639
0.5085	Remote Similarity	NPC311178
0.5085	Remote Similarity	NPC478559
0.5085	Remote Similarity	NPC478560
0.508	Remote Similarity	NPC488513
0.5068	Remote Similarity	NPC232237
0.5068	Remote Similarity	NPC469946
0.5062	Remote Similarity	NPC473452
0.5055	Remote Similarity	NPC481323
0.5054	Remote Similarity	NPC481324
0.5053	Remote Similarity	NPC476113
0.5034	Remote Similarity	NPC112352
0.5032	Remote Similarity	NPC155410
0.5031	Remote Similarity	NPC471580
0.5031	Remote Similarity	NPC470876
0.5031	Remote Similarity	NPC258617
0.5029	Remote Similarity	NPC329893

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC472269 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	8011
0.1-0.2	1113
0.2-0.3	24
0.3-0.4	2
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