NPASS Compound

Natural Product: NPC231888

Natural Product ID	NPC231888
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	Pescaprein Xxv
IUPAC Name	n.a.
Synonyms	Pescaprein XXV
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL1773741
PubChem CID	52952426
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0004603] Organic oxygen compounds [CHEMONTID:0000323] Organooxygen compounds [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates [CHEMONTID:0000198] Oligosaccharides

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

Chemical Representations

RDKit 2D 210216 0 0 0 0 0 0 0 0999 V2000 21.7981 -2.9544 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 20.2981 -2.9544 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 18.7981 -2.9544 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 17.2981 -2.9544 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 15.7981 -2.9544 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 14.2981 -2.9544 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 12.7981 -2.9544 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 11.2981 -2.9544 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.7981 -2.9544 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.2981 -2.9544 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.7981 -2.9544 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2981 -2.9544 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3954 -1.7565 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.5481 -4.2535 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.0481 -4.2535 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3086 -5.7307 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1595 -6.6949 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7500 -6.1818 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7500 -6.1818 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4895 -4.7046 0.0000 O 0 0 0 0 0 0 0 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54173 1 0 56174 1 0 57175 1 0 59176 1 0 61177 1 6 62178 1 1 63179 1 1 64180 1 6 65181 1 1 66182 1 0 66183 1 0 66184 1 0 71185 1 0 72186 1 0 72187 1 0 72188 1 0 73189 1 0 73190 1 0 73191 1 0 77192 1 0 78193 1 0 80194 1 0 81195 1 0 82196 1 0 83197 1 0 84198 1 0 85199 1 0 87200 1 1 88201 1 6 89202 1 6 90203 1 1 91204 1 6 92205 1 0 92206 1 0 92207 1 0 94208 1 0 95209 1 0 96210 1 0 M END

Standard InCHIKey	GEIFMZOIUWDOQZ-DQRIPJEXSA-N
Standard InCHI	InChI=1S/C71H114O25/c1-10-12-14-15-16-17-20-23-31-37-49(73)91-65-64(96-67-55(79)53(77)51(75)41(5)83-67)60(93-68-56(80)61(58(43(7)85-68)92-66(82)40(3)4)90-50(74)39-38-46-32-27-25-28-33-46)45(9)87-71(65)94-59-44(8)86-69-57(81)62(59)89-48(72)36-30-24-21-18-19-22-29-35-47(34-26-13-11-2)88-70-63(95-69)54(78)52(76)42(6)84-70/h25,27-28,32-33,38-45,47,51-65,67-71,75-81H,10-24,26,29-31,34-37H2,1-9H3/b39-38+/t41-,42+,43-,44-,45-,47-,51-,52-,53+,54-,55+,56+,57+,58-,59-,60-,61-,62-,63+,64+,65+,67-,68-,69-,70-,71-/m0/s1
SMILES	CCCCCCCCCCCC(=O)O[C@@H]1[C@@H]([C@H]([C@H](C)O[C@H]1O[C@H]1[C@H](C)O[C@@H]2[C@@H]([C@@H]1OC(=O)CCCCCCCCC[C@H](CCCCC)O[C@H]1[C@@H]([C@H]([C@H]([C@@H](C)O1)O)O)O2)O)O[C@H]1[C@@H]([C@@H]([C@H]([C@H](C)O1)OC(=O)C(C)C)OC(=O)/C=C/c1ccccc1)O)O[C@H]1[C@@H]([C@@H]([C@H]([C@H](C)O1)O)O)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	1366.76	Volume:	1375.34 ? Van der Waals volume.
Dense:	0.994	LogP:	6.5 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	5.111 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-5.52 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	29.0	Rigid Bonds:	57.0
TPSA:	339.11 ? Topological Polar Surface Area.	H-Bond Acceptor:	25.0
H-Bond Donor:	7.0	Rings:	7.0
Heavy Atoms:	25.0

MedChem Properties

QED Drug-Likeness Score:	0.021	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	6.773	Fsp³:	0.831
MCE-18:	187.538 ? 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:	1.0	Fluc inhibitor:	0.666 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.233 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.315 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.384	Promiscuous compounds:	0.006

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.512	MDCK Permeability:	-5.02
Pgp-inhibitor:	0.018	Pgp-substrate:	0.918
PAMPA:	0.95 ? 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):	0.052
20% Bioavailability (F20%):	0.564	30% Bioavailability (F30%):	0.979
50% Bioavailability (F50%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.0	MRP1:	0.996
Plasma Protein Binding (PPB):	97.277%	Volume Distribution (VD):	0.03
Fu:	1.42% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.862
OATP1B3 inhibitor:	1.0	BCRP inhibitor:	0.0
BSEP inhibitor:	0.995

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.029
CYP2C19-inhibitor:	0.0	CYP2C19-substrate:	0.0
CYP2C9-inhibitor:	0.0	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.572
CYP3A4-inhibitor:	0.0	CYP3A4-substrate:	1.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	1.0
HLM stability:	0.87 ? 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):

0.767

Half-life (T1/2):

3.965

ADMET: Toxicity

hERG Blockers:	0.115	hERG Blockers (10um):	0.403
Human Hepatotoxicity (H-HT):	0.578	Drug-induced Liver Injury (DILI):	0.997
AMES Toxicity:	0.649	Rat Oral Acute Toxicity:	0.001
Maximum Recommended Daily Dose:	0.003	Skin Sensitization:	1.0
Carcinogencity:	0.0	Eye Corrosion:	0.0
Eye Irritation:	0.001	Respiratory Toxicity:	0.001
Drug-induced Neurotoxicity:	0.0	Ototoxicity:	0.998
Hematotoxicity:	0.623	Drug-induced Nephrotoxicity:	0.982
Genotoxicity:	0.0	RPMI-8226 Immunitoxicity:	0.741
A549 Cytotoxicity:	1.0	Hek293 Cytotoxicity:	0.824
BCF:	0.727 ? 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:	5.082 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	6.534 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	5.532 ? 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
NPO23352	Ipomoea pes-caprae	Species	Convolvulaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15730248]
NPO23352	Ipomoea pes-caprae	Species	Convolvulaceae	Eukaryota	Leaves	Khon Kaen, Thailand	2002-APR	PMID[15921434]
NPO23352	Ipomoea pes-caprae	Species	Convolvulaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19061389]
NPO23352	Ipomoea pes-caprae	Species	Convolvulaceae	Eukaryota	ground entire plants	Hainan Province, China	2004-APR	PMID[19061389]
NPO23352	Ipomoea pes-caprae	Species	Convolvulaceae	Eukaryota	n.a.	aerial part	n.a.	PMID[21338052]
NPO23352	Ipomoea pes-caprae	Species	Convolvulaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[31017778]
NPO23352	Ipomoea pes-caprae	Species	Convolvulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO23352	Ipomoea pes-caprae	Species	Convolvulaceae	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
Ratio IC50	1
Activity	4
IC50	2

Activity Type	# Activity
Cell line	4
Unchecked	2
Others	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
NPT389	Cell line	RPMI-8226	Homo sapiens	IC50	>	10000.0	nM	PMID[34969245]
NPT28438	Unchecked	Unchecked	n.a.	Activity	n.a.	n.a.	n.a.	PMID[34969245]
NPT25439	Cell line	MM1.S	Homo sapiens	Activity	n.a.	n.a.	n.a.	PMID[34969245]
NPT2	Others	Unspecified	n.a.	Ratio IC50	=	2.1	n.a.	PMID[21338052]

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 NPC231888 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	13928
0.1-0.2	32013
0.2-0.3	3578
0.3-0.4	208
0.4-0.5	55
0.5-0.6	38
0.6-0.7	15
0.7-0.8	0
0.8-0.85	3
0.85-0.9	0
0.9-0.95	4
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC124878
0.9444	High Similarity	NPC35338
0.9444	High Similarity	NPC204214
0.9444	High Similarity	NPC92283
0.9231	High Similarity	NPC63404
0.8454	Intermediate Similarity	NPC10121
0.8454	Intermediate Similarity	NPC198918
0.8265	Intermediate Similarity	NPC10883
0.76	Intermediate Similarity	NPC77651
0.7391	Intermediate Similarity	NPC267592
0.7356	Intermediate Similarity	NPC146380
0.7321	Intermediate Similarity	NPC147032
0.7087	Intermediate Similarity	NPC28069
0.7083	Intermediate Similarity	NPC290012
0.7053	Intermediate Similarity	NPC307400
0.7053	Intermediate Similarity	NPC27289
0.7033	Intermediate Similarity	NPC113745
0.7033	Intermediate Similarity	NPC477320
0.7033	Intermediate Similarity	NPC477323
0.7033	Intermediate Similarity	NPC477325
0.7033	Intermediate Similarity	NPC609436
0.7	Intermediate Similarity	NPC471024
0.6957	Remote Similarity	NPC604005
0.6957	Remote Similarity	NPC605014
0.6947	Remote Similarity	NPC477319
0.6916	Remote Similarity	NPC471025
0.6907	Remote Similarity	NPC162925
0.6887	Remote Similarity	NPC290276
0.6875	Remote Similarity	NPC143421
0.6875	Remote Similarity	NPC472204
0.6768	Remote Similarity	NPC123204
0.65	Remote Similarity	NPC183888
0.65	Remote Similarity	NPC259294
0.6458	Remote Similarity	NPC477326
0.6337	Remote Similarity	NPC126685
0.6277	Remote Similarity	NPC281563
0.604	Remote Similarity	NPC294748
0.598	Remote Similarity	NPC483170
0.5979	Remote Similarity	NPC87153
0.596	Remote Similarity	NPC600446
0.596	Remote Similarity	NPC605013
0.5922	Remote Similarity	NPC115013
0.5859	Remote Similarity	NPC89843
0.5842	Remote Similarity	NPC146992
0.5842	Remote Similarity	NPC85759
0.5816	Remote Similarity	NPC22742
0.5816	Remote Similarity	NPC477346
0.5812	Remote Similarity	NPC471026
0.5789	Remote Similarity	NPC477350
0.5769	Remote Similarity	NPC169345
0.5728	Remote Similarity	NPC119583
0.5619	Remote Similarity	NPC238056
0.5579	Remote Similarity	NPC606819
0.55	Remote Similarity	NPC477349
0.549	Remote Similarity	NPC158302
0.5481	Remote Similarity	NPC173328
0.5463	Remote Similarity	NPC44782
0.5437	Remote Similarity	NPC109887
0.5437	Remote Similarity	NPC478733
0.5429	Remote Similarity	NPC186992
0.534	Remote Similarity	NPC477344
0.5333	Remote Similarity	NPC472205
0.5327	Remote Similarity	NPC477317
0.5327	Remote Similarity	NPC477318
0.5278	Remote Similarity	NPC184915
0.5278	Remote Similarity	NPC224953
0.5243	Remote Similarity	NPC478734
0.514	Remote Similarity	NPC478730
0.5133	Remote Similarity	NPC140561
0.5093	Remote Similarity	NPC238264
0.5093	Remote Similarity	NPC477345
0.5091	Remote Similarity	NPC475525
0.5091	Remote Similarity	NPC475540
0.5047	Remote Similarity	NPC297768
0.5041	Remote Similarity	NPC472352

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC231888 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4767
0.1-0.2	4321
0.2-0.3	60
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