NPASS Compound

Natural Product: NPC545712

Natural Product ID	NPC545712
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	Cabucine
IUPAC Name	methyl (1~{S},15~{R},16~{S},20~{S})-7-methoxy-16-methyl-17-oxa-3,13-diazapentacyclo[11.8.0.0^{2,10}.0^{4,9}.0^{15,20}]henicosa-2(10),4,6,8,18-pentaene-19-carboxylate
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
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 54 58 0 0 0 0 0 0 0 0999 V2000 -5.9945 -3.3735 -0.0389 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.5232 -2.1077 -0.4531 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.2594 -1.6507 -0.0287 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6358 -2.4499 0.7163 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.7440 -0.3569 -0.4344 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.4793 0.4049 -1.2152 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0616 1.6647 -1.6535 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.0264 2.3628 -0.9337 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.5818 3.0066 0.2896 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9628 1.3618 -0.6841 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.7596 1.8307 0.0438 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4232 1.0000 1.1720 N 0 0 0 0 0 0 0 0 0 0 0 0 0.7083 1.5197 1.9003 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9756 1.5013 1.0906 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1719 0.1557 0.5383 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1228 -0.7204 0.4402 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6104 -1.8527 -0.0973 N 0 0 0 0 0 0 0 0 0 0 0 0 2.9241 -1.7171 -0.3385 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8659 -2.5679 -0.8705 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1898 -2.1949 -1.0241 C 0 0 0 0 0 0 0 0 0 0 0 0 5.5576 -0.9172 -0.6221 C 0 0 0 0 0 0 0 0 0 0 0 0 6.8933 -0.5348 -0.7748 O 0 0 0 0 0 0 0 0 0 0 0 0 7.2559 0.7608 -0.3649 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6324 -0.0510 -0.0880 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3257 -0.4659 0.0459 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2506 -0.3945 0.8703 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.2991 -0.8609 -0.1338 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4444 0.0933 0.0078 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.3239 -3.3879 1.0187 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.1836 -4.1371 -0.1432 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.8169 -3.6549 -0.7402 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.4483 0.0730 -1.5483 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6552 3.1253 -1.6222 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6564 2.2898 1.1249 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0125 3.9155 0.5420 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.6188 3.3682 0.0326 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6124 1.0055 -1.6994 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1424 1.9216 -0.6237 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9448 2.8447 0.4272 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8764 0.8153 2.7651 H 0 0 0 0 0 0 0 0 0 0 0 0 0.4685 2.4894 2.3420 H 0 0 0 0 0 0 0 0 0 0 0 0 1.9053 2.3000 0.3264 H 0 0 0 0 0 0 0 0 0 0 0 0 2.8118 1.7026 1.8112 H 0 0 0 0 0 0 0 0 0 0 0 0 1.0449 -2.7208 -0.3001 H 0 0 0 0 0 0 0 0 0 0 0 0 3.6277 -3.5828 -1.2018 H 0 0 0 0 0 0 0 0 0 0 0 0 5.9255 -2.8673 -1.4427 H 0 0 0 0 0 0 0 0 0 0 0 0 7.1308 0.8937 0.7202 H 0 0 0 0 0 0 0 0 0 0 0 0 6.6847 1.5374 -0.9395 H 0 0 0 0 0 0 0 0 0 0 0 0 8.3592 0.8644 -0.5735 H 0 0 0 0 0 0 0 0 0 0 0 0 4.8875 0.9473 0.2332 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5208 -0.9438 1.8229 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5201 -1.9149 -0.0553 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8078 -0.7080 -1.1407 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5312 0.3777 1.0975 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 3 5 1 0 5 6 2 0 6 7 1 0 7 8 1 0 8 9 1 0 8 10 1 0 10 11 1 0 11 12 1 0 12 13 1 0 13 14 1 0 14 15 1 0 15 16 2 0 16 17 1 0 17 18 1 0 18 19 2 0 19 20 1 0 20 21 2 0 21 22 1 0 22 23 1 0 21 24 1 0 24 25 2 0 16 26 1 0 26 27 1 0 27 28 1 0 28 5 1 0 28 10 1 0 26 12 1 0 25 15 1 0 25 18 1 0 1 29 1 0 1 30 1 0 1 31 1 0 6 32 1 0 8 33 1 6 9 34 1 0 9 35 1 0 9 36 1 0 10 37 1 6 11 38 1 0 11 39 1 0 13 40 1 0 13 41 1 0 14 42 1 0 14 43 1 0 17 44 1 0 19 45 1 0 20 46 1 0 23 47 1 0 23 48 1 0 23 49 1 0 24 50 1 0 26 51 1 1 27 52 1 0 27 53 1 0 28 54 1 1 M END

Standard InCHIKey	DTDADHMBRZKXSC-IEGSVRCHSA-N
Standard InCHI	InChI=1S/C22H26N2O4/c1-12-17-10-24-7-6-14-16-8-13(26-2)4-5-19(16)23-21(14)20(24)9-15(17)18(11-28-12)22(25)27-3/h4-5,8,11-12,15,17,20,23H,6-7,9-10H2,1-3H3/t12-,15-,17+,20-/m0/s1
SMILES	COC(=O)C1=CO[C@@H](C)[C@H]2CN3CCC4=C(NC5=CC=C(OC)C=C45)[C@@H]3C[C@H]12

Calculated Properties

Physi-Chem Properties

Molecular Weight:	382.19	Volume:	387.622 ? Van der Waals volume.
Dense:	0.986	LogP:	2.429 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	2.419 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-3.385 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	3.0	Rigid Bonds:	26.0
TPSA:	63.79 ? Topological Polar Surface Area.	H-Bond Acceptor:	6.0
H-Bond Donor:	1.0	Rings:	5.0
Heavy Atoms:	6.0

MedChem Properties

QED Drug-Likeness Score:	0.809	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	3.979	Fsp³:	0.5
MCE-18:	94.091 ? 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:	Rejected
Golden Triangle Rule:	Rejected	BMS Rule:	0
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.214	Fluc inhibitor:	0.315 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.881 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.149 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.002	Promiscuous compounds:	0.523

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-4.819	MDCK Permeability:	-4.828
Pgp-inhibitor:	0.185	Pgp-substrate:	0.482
PAMPA:	0.003 ? 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):	0.001
20% Bioavailability (F20%):	0.546	30% Bioavailability (F30%):	0.694
50% Bioavailability (F50%):	0.985

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.151	MRP1:	0.999
Plasma Protein Binding (PPB):	81.489%	Volume Distribution (VD):	0.507
Fu:	20.629% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.747
OATP1B3 inhibitor:	0.903	BCRP inhibitor:	0.954
BSEP inhibitor:	0.996

ADMET: Metabolism

CYP1A2-inhibitor:	1.0	CYP1A2-substrate:	0.354
CYP2C19-inhibitor:	0.947	CYP2C19-substrate:	0.66
CYP2C9-inhibitor:	0.0	CYP2C9-substrate:	0.989
CYP2D6-inhibitor:	0.95	CYP2D6-substrate:	0.964
CYP3A4-inhibitor:	1.0	CYP3A4-substrate:	1.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.992
HLM stability:	0.092 ? 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):

10.962

Half-life (T1/2):

1.393

ADMET: Toxicity

hERG Blockers:	0.723	hERG Blockers (10um):	0.609
Human Hepatotoxicity (H-HT):	0.557	Drug-induced Liver Injury (DILI):	0.766
AMES Toxicity:	0.747	Rat Oral Acute Toxicity:	0.839
Maximum Recommended Daily Dose:	0.983	Skin Sensitization:	0.278
Carcinogencity:	0.828	Eye Corrosion:	0.0
Eye Irritation:	0.12	Respiratory Toxicity:	0.978
Drug-induced Neurotoxicity:	0.85	Ototoxicity:	0.583
Hematotoxicity:	0.314	Drug-induced Nephrotoxicity:	0.917
Genotoxicity:	0.98	RPMI-8226 Immunitoxicity:	0.093
A549 Cytotoxicity:	0.603	Hek293 Cytotoxicity:	0.679
BCF:	1.065 ? 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:	3.747 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.285 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.614 ? 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
NPO12952	Cabucala madagascariensis	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO63206	Rauwolfia media	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[COCONUT]
NPO12952	Cabucala madagascariensis	Species	Apocynaceae	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 NPC545712 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	18731
0.1-0.2	30397
0.2-0.3	603
0.3-0.4	72
0.4-0.5	33
0.5-0.6	10
0.6-0.7	5
0.7-0.8	2
0.8-0.85	1
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	NPC603895
0.8101	Intermediate Similarity	NPC21638
0.7949	Intermediate Similarity	NPC312870
0.7949	Intermediate Similarity	NPC199851
0.7949	Intermediate Similarity	NPC294909
0.7949	Intermediate Similarity	NPC254240
0.7949	Intermediate Similarity	NPC128265
0.7949	Intermediate Similarity	NPC604675
0.6118	Remote Similarity	NPC486449
0.6118	Remote Similarity	NPC63199
0.6118	Remote Similarity	NPC111602
0.6118	Remote Similarity	NPC102338
0.6118	Remote Similarity	NPC196251
0.5977	Remote Similarity	NPC100898
0.5977	Remote Similarity	NPC148183
0.5977	Remote Similarity	NPC21084
0.5977	Remote Similarity	NPC152768
0.5977	Remote Similarity	NPC605270
0.593	Remote Similarity	NPC273374
0.5795	Remote Similarity	NPC131260
0.5326	Remote Similarity	NPC293861
0.5165	Remote Similarity	NPC107782
0.5165	Remote Similarity	NPC486454

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC545712 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	3690
0.1-0.2	5326
0.2-0.3	122
0.3-0.4	3
0.4-0.5	7
0.5-0.6	0
0.6-0.7	0
0.7-0.8	2
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
0.7949	Intermediate Similarity	NPD4500	Approved
0.7949	Intermediate Similarity	NPD4501	Approved

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