NPASS Compound

Natural Product: NPC35338

Natural Product ID	NPC35338
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	Pescaprein Xxiii
IUPAC Name	n.a.
Synonyms	Pescaprein XXIII
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL1773739
PubChem CID	52952310
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 207213 0 0 0 0 0 0 0 0999 V2000 -6.2605 9.5848 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.5105 8.2858 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.7605 6.9867 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0105 5.6877 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2605 4.3887 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5105 3.0896 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7605 1.7906 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0105 0.4915 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2605 -0.8075 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4895 -2.1065 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9783 -2.2894 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.2605 -3.4056 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.4895 -4.7046 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6386 -3.7404 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0481 -4.2535 0.0000 O 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 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.5000 -7.4809 0.0000 C 0 0 0 0 0 0 0 0 0 0 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77184 1 0 78185 1 1 80186 1 1 81187 1 6 83188 1 1 84189 1 0 85190 1 1 86191 1 1 88192 1 0 88193 1 0 88194 1 0 89195 1 0 90196 1 0 90197 1 0 91198 1 0 91199 1 0 92200 1 0 92201 1 0 93202 1 0 93203 1 0 94204 1 0 94205 1 0 94206 1 0 95207 1 0 M END

Standard InCHIKey	VCBSNBJPLWMYQG-JEENFSGDSA-N
Standard InCHI	InChI=1S/C70H112O25/c1-10-13-15-16-18-22-30-36-48(72)90-64-63(95-66-54(78)52(76)50(74)40(5)82-66)59(92-67-55(79)60(57(42(7)84-67)91-65(81)39(4)12-3)89-49(73)38-37-45-31-26-24-27-32-45)44(9)86-70(64)93-58-43(8)85-68-56(80)61(58)88-47(71)35-29-23-20-17-19-21-28-34-46(33-25-14-11-2)87-69-62(94-68)53(77)51(75)41(6)83-69/h24,26-27,31-32,37-44,46,50-64,66-70,74-80H,10-23,25,28-30,33-36H2,1-9H3/b38-37+/t39-,40-,41+,42-,43-,44-,46-,50-,51-,52+,53-,54+,55+,56+,57-,58-,59-,60-,61-,62+,63+,64+,66-,67-,68-,69-,70-/m0/s1
SMILES	CCCCCCCCCC(=O)O[C@H]1[C@@H](O[C@H]([C@@H]([C@H]1O[C@@H]1O[C@@H](C)[C@@H]([C@H]([C@H]1O)O)O)O[C@@H]1O[C@@H](C)[C@@H]([C@H]([C@H]1O)OC(=O)/C=C/c1ccccc1)OC(=O)[C@H](CC)C)C)O[C@H]1[C@H](C)O[C@@H]2[C@@H]([C@@H]1OC(=O)CCCCCCCCC[C@@H](O[C@H]1[C@H](O2)[C@@H](O)[C@H]([C@H](O1)C)O)CCCCC)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	1352.75	Volume:	1358.044 ? Van der Waals volume.
Dense:	0.996	LogP:	6.046 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	4.883 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-5.329 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	28.0	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:	0.023	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	6.786	Fsp³:	0.829
MCE-18:	187.984 ? 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:	0.219 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.318 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.382	Promiscuous compounds:	0.016

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.568	MDCK Permeability:	-5.02
Pgp-inhibitor:	0.011	Pgp-substrate:	0.972
PAMPA:	0.996 ? 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%):	0.149	30% Bioavailability (F30%):	0.908
50% Bioavailability (F50%):	0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.0	MRP1:	0.987
Plasma Protein Binding (PPB):	96.472%	Volume Distribution (VD):	-0.152
Fu:	2.841% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.954
OATP1B3 inhibitor:	1.0	BCRP inhibitor:	0.0
BSEP inhibitor:	0.955

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.033
CYP2C19-inhibitor:	0.0	CYP2C19-substrate:	0.0
CYP2C9-inhibitor:	0.0	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.172
CYP3A4-inhibitor:	0.0	CYP3A4-substrate:	1.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	1.0
HLM stability:	0.972 ? 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):

0.65

Half-life (T1/2):

3.557

ADMET: Toxicity

hERG Blockers:	0.084	hERG Blockers (10um):	0.317
Human Hepatotoxicity (H-HT):	0.533	Drug-induced Liver Injury (DILI):	0.995
AMES Toxicity:	0.688	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:	0.002	Respiratory Toxicity:	0.001
Drug-induced Neurotoxicity:	0.0	Ototoxicity:	0.997
Hematotoxicity:	0.692	Drug-induced Nephrotoxicity:	0.985
Genotoxicity:	0.0	RPMI-8226 Immunitoxicity:	0.789
A549 Cytotoxicity:	0.999	Hek293 Cytotoxicity:	0.777
BCF:	0.635 ? 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:	4.675 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	6.203 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	5.25 ? 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	=	2.9	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 NPC35338 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	13880
0.1-0.2	31899
0.2-0.3	3731
0.3-0.4	217
0.4-0.5	45
0.5-0.6	39
0.6-0.7	26
0.7-0.8	0
0.8-0.85	0
0.85-0.9	3
0.9-0.95	2
0.95-1	3

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC204214
1.0	High Similarity	NPC92283
0.9775	High Similarity	NPC63404
0.9444	High Similarity	NPC124878
0.9444	High Similarity	NPC231888
0.8947	High Similarity	NPC10121
0.8947	High Similarity	NPC198918
0.875	High Similarity	NPC10883
0.7727	Intermediate Similarity	NPC147032
0.7527	Intermediate Similarity	NPC307400
0.7527	Intermediate Similarity	NPC27289
0.7525	Intermediate Similarity	NPC77651
0.7419	Intermediate Similarity	NPC477319
0.7407	Intermediate Similarity	NPC471024
0.734	Intermediate Similarity	NPC143421
0.734	Intermediate Similarity	NPC472204
0.7308	Intermediate Similarity	NPC290276
0.7273	Intermediate Similarity	NPC146380
0.7216	Intermediate Similarity	NPC123204
0.7188	Intermediate Similarity	NPC290012
0.7019	Intermediate Similarity	NPC28069
0.6957	Remote Similarity	NPC113745
0.6957	Remote Similarity	NPC477320
0.6957	Remote Similarity	NPC477323
0.6957	Remote Similarity	NPC477325
0.6957	Remote Similarity	NPC609436
0.6947	Remote Similarity	NPC267592
0.6939	Remote Similarity	NPC183888
0.6939	Remote Similarity	NPC259294
0.6882	Remote Similarity	NPC604005
0.6882	Remote Similarity	NPC605014
0.6852	Remote Similarity	NPC471025
0.6837	Remote Similarity	NPC162925
0.6768	Remote Similarity	NPC126685
0.64	Remote Similarity	NPC483170
0.6392	Remote Similarity	NPC477326
0.6289	Remote Similarity	NPC89843
0.6263	Remote Similarity	NPC146992
0.6263	Remote Similarity	NPC85759
0.625	Remote Similarity	NPC22742
0.625	Remote Similarity	NPC477346
0.6211	Remote Similarity	NPC281563
0.6176	Remote Similarity	NPC169345
0.6139	Remote Similarity	NPC294748
0.6139	Remote Similarity	NPC119583
0.6019	Remote Similarity	NPC238056
0.6019	Remote Similarity	NPC115013
0.5918	Remote Similarity	NPC87153
0.59	Remote Similarity	NPC158302
0.59	Remote Similarity	NPC600446
0.59	Remote Similarity	NPC605013
0.5882	Remote Similarity	NPC173328
0.5763	Remote Similarity	NPC471026
0.5743	Remote Similarity	NPC477344
0.5729	Remote Similarity	NPC477350
0.5728	Remote Similarity	NPC472205
0.5714	Remote Similarity	NPC477317
0.5714	Remote Similarity	NPC477318
0.5673	Remote Similarity	NPC186992
0.566	Remote Similarity	NPC184915
0.566	Remote Similarity	NPC224953
0.5644	Remote Similarity	NPC478734
0.5556	Remote Similarity	NPC44782
0.5534	Remote Similarity	NPC478733
0.5521	Remote Similarity	NPC606819
0.5472	Remote Similarity	NPC238264
0.5472	Remote Similarity	NPC477345
0.5446	Remote Similarity	NPC477349
0.5429	Remote Similarity	NPC297768
0.5385	Remote Similarity	NPC109887
0.5372	Remote Similarity	NPC472352
0.5327	Remote Similarity	NPC476087
0.5327	Remote Similarity	NPC475667
0.5278	Remote Similarity	NPC478732
0.5273	Remote Similarity	NPC269318
0.5229	Remote Similarity	NPC475270
0.5229	Remote Similarity	NPC475327
0.5225	Remote Similarity	NPC475164
0.5192	Remote Similarity	NPC477331
0.5088	Remote Similarity	NPC140561
0.5088	Remote Similarity	NPC475241
0.5045	Remote Similarity	NPC163409
0.5045	Remote Similarity	NPC472200
0.5044	Remote Similarity	NPC473605
0.5044	Remote Similarity	NPC475375
0.5041	Remote Similarity	NPC600940

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC35338 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4818
0.1-0.2	4262
0.2-0.3	68
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