NPASS Compound

Natural Product: NPC523632

Natural Product ID	NPC523632
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	methyl (2~{S},12~{b}~{S})-2-[1-(hydroxymethyl)prop-1-enyl]-1,2,6,7,12,12~{b}-hexahydroindolo[2,3-a]quinolizine-3-carboxylate
IUPAC Name	methyl (2~{S},12~{b}~{S})-2-[1-(hydroxymethyl)prop-1-enyl]-1,2,6,7,12,12~{b}-hexahydroindolo[2,3-a]quinolizine-3-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 50 53 0 0 0 0 0 0 0 0999 V2000 -3.3580 -3.1360 -0.4707 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5695 -2.1021 0.2417 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1593 -0.9855 -0.4032 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5306 -0.8495 -1.8314 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2859 0.2503 -2.1249 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.3029 -0.0834 0.3358 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.3636 -0.6956 1.3405 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8105 0.2478 1.5696 C 0 0 1 0 0 0 0 0 0 0 0 0 2.0029 -0.2538 0.8553 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6033 0.4382 -0.1752 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1026 1.7539 -0.6532 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5427 2.4418 0.5752 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4935 1.5834 1.0773 N 0 0 0 0 0 0 0 0 0 0 0 0 -0.8251 2.0816 1.1021 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8040 1.2123 0.7169 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1693 1.6404 0.7980 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1256 0.9181 0.5090 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.4941 2.9440 1.2239 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.8359 3.3779 1.3080 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6699 -0.3284 -0.5919 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6039 -0.1105 -1.5868 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6018 -1.0240 -1.8376 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6595 -2.1781 -1.0719 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7283 -2.3959 -0.0795 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7213 -1.4921 0.1864 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7091 -1.4089 1.0383 N 0 0 0 0 0 0 0 0 0 0 0 0 -2.8070 -3.5654 -1.3315 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3246 -2.7501 -0.8664 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6377 -3.9791 0.1924 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3436 -2.2811 1.2802 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6231 -0.9057 -2.4898 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1352 -1.7455 -2.1675 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.8101 0.0774 -2.9608 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5179 0.2303 -0.5349 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0265 -1.6536 0.9883 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8937 -0.8425 2.2849 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9830 0.3381 2.6495 H 0 0 0 0 0 0 0 0 0 0 0 0 1.2639 1.5799 -1.3500 H 0 0 0 0 0 0 0 0 0 0 0 0 2.9120 2.3547 -1.1232 H 0 0 0 0 0 0 0 0 0 0 0 0 2.3443 2.5277 1.3478 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1846 3.4624 0.3553 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0772 3.0737 1.3979 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.5141 2.8153 0.6492 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.9373 4.4649 1.0907 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.1209 3.2711 2.3928 H 0 0 0 0 0 0 0 0 0 0 0 0 4.5419 0.8030 -2.1783 H 0 0 0 0 0 0 0 0 0 0 0 0 6.2973 -0.7966 -2.6246 H 0 0 0 0 0 0 0 0 0 0 0 0 6.4580 -2.8693 -1.3008 H 0 0 0 0 0 0 0 0 0 0 0 0 4.8131 -3.3083 0.4907 H 0 0 0 0 0 0 0 0 0 0 0 0 2.4925 -2.1472 1.7563 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 2 3 3 4 1 0 4 5 1 0 3 6 1 0 6 7 1 0 7 8 1 0 8 9 1 0 9 10 2 0 10 11 1 0 11 12 1 0 12 13 1 0 13 14 1 0 14 15 2 0 15 16 1 0 16 17 2 0 16 18 1 0 18 19 1 0 10 20 1 0 20 21 2 0 21 22 1 0 22 23 2 0 23 24 1 0 24 25 2 0 25 26 1 0 15 6 1 0 25 20 1 0 13 8 1 0 26 9 1 0 1 27 1 0 1 28 1 0 1 29 1 0 2 30 1 0 4 31 1 0 4 32 1 0 5 33 1 0 6 34 1 6 7 35 1 0 7 36 1 0 8 37 1 1 11 38 1 0 11 39 1 0 12 40 1 0 12 41 1 0 14 42 1 0 19 43 1 0 19 44 1 0 19 45 1 0 21 46 1 0 22 47 1 0 23 48 1 0 24 49 1 0 26 50 1 0 M END

Standard InCHIKey	FRUFGLJBMBUARK-LPHOPBHVSA-N
Standard InCHI	InChI=1S/C21H24N2O3/c1-3-13(12-24)16-10-19-20-15(14-6-4-5-7-18(14)22-20)8-9-23(19)11-17(16)21(25)26-2/h3-7,11,16,19,22,24H,8-10,12H2,1-2H3/t16-,19-/m0/s1
SMILES	CC=C(CO)[C@@H]1C[C@H]2C3=C(CCN2C=C1C(=O)OC)C1=CC=CC=C1N3

Calculated Properties

Physi-Chem Properties

Molecular Weight:	352.18	Volume:	367.455 ? Van der Waals volume.
Dense:	0.958	LogP:	2.383 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	2.46 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-3.46 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	4.0	Rigid Bonds:	22.0
TPSA:	65.56 ? Topological Polar Surface Area.	H-Bond Acceptor:	5.0
H-Bond Donor:	2.0	Rings:	4.0
Heavy Atoms:	5.0

MedChem Properties

QED Drug-Likeness Score:	0.658	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	3.903	Fsp³:	0.381
MCE-18:	73.586 ? 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:	0.28	Fluc inhibitor:	0.615 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.793 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.513 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.002	Promiscuous compounds:	0.393

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.138	MDCK Permeability:	-4.746
Pgp-inhibitor:	0.016	Pgp-substrate:	0.603
PAMPA:	0.765 ? 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):	0.0
20% Bioavailability (F20%):	0.034	30% Bioavailability (F30%):	0.178
50% Bioavailability (F50%):	0.927

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.69	MRP1:	0.997
Plasma Protein Binding (PPB):	92.474%	Volume Distribution (VD):	0.326
Fu:	6.956% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.829
OATP1B3 inhibitor:	0.984	BCRP inhibitor:	0.867
BSEP inhibitor:	0.987

ADMET: Metabolism

CYP1A2-inhibitor:	0.472	CYP1A2-substrate:	0.209
CYP2C19-inhibitor:	0.913	CYP2C19-substrate:	0.3
CYP2C9-inhibitor:	0.002	CYP2C9-substrate:	0.076
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.328
CYP3A4-inhibitor:	1.0	CYP3A4-substrate:	0.998
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.999
HLM stability:	0.655 ? 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):

8.453

Half-life (T1/2):

0.646

ADMET: Toxicity

hERG Blockers:	0.346	hERG Blockers (10um):	0.438
Human Hepatotoxicity (H-HT):	0.879	Drug-induced Liver Injury (DILI):	0.911
AMES Toxicity:	0.591	Rat Oral Acute Toxicity:	0.846
Maximum Recommended Daily Dose:	0.968	Skin Sensitization:	0.894
Carcinogencity:	0.753	Eye Corrosion:	0.0
Eye Irritation:	0.104	Respiratory Toxicity:	0.952
Drug-induced Neurotoxicity:	0.834	Ototoxicity:	0.95
Hematotoxicity:	0.416	Drug-induced Nephrotoxicity:	0.975
Genotoxicity:	0.995	RPMI-8226 Immunitoxicity:	0.113
A549 Cytotoxicity:	0.153	Hek293 Cytotoxicity:	0.316
BCF:	0.751 ? 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:	3.542 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.2 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.477 ? 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
NPO3893	Chimarrhis turbinata	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15568781]
NPO3893	Chimarrhis turbinata	Species	Rubiaceae	Eukaryota	leaves	n.a.	n.a.	PMID[21341711]
NPO3893	Chimarrhis turbinata	Species	Rubiaceae	Eukaryota	n.a.	leaf	n.a.	PMID[21341711]
NPO3893	Chimarrhis turbinata	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO3893	Chimarrhis turbinata	Species	Rubiaceae	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 NPC523632 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	10733
0.1-0.2	37822
0.2-0.3	993
0.3-0.4	217
0.4-0.5	53
0.5-0.6	35
0.6-0.7	4
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
0.8571	High Similarity	NPC220151
0.8571	High Similarity	NPC19692
0.642	Remote Similarity	NPC107782
0.642	Remote Similarity	NPC486454
0.622	Remote Similarity	NPC175474
0.622	Remote Similarity	NPC99921
0.5783	Remote Similarity	NPC486452
0.5783	Remote Similarity	NPC74591
0.5714	Remote Similarity	NPC486449
0.5714	Remote Similarity	NPC63199
0.5714	Remote Similarity	NPC111602
0.5714	Remote Similarity	NPC102338
0.5714	Remote Similarity	NPC486443
0.5714	Remote Similarity	NPC486446
0.5714	Remote Similarity	NPC196251
0.5714	Remote Similarity	NPC273374
0.5641	Remote Similarity	NPC21174
0.5625	Remote Similarity	NPC165441
0.5517	Remote Similarity	NPC312870
0.5517	Remote Similarity	NPC199851
0.5517	Remote Similarity	NPC294909
0.5517	Remote Similarity	NPC254240
0.5517	Remote Similarity	NPC128265
0.5517	Remote Similarity	NPC604675
0.5402	Remote Similarity	NPC52557
0.5402	Remote Similarity	NPC217463
0.5349	Remote Similarity	NPC313985
0.5349	Remote Similarity	NPC249150
0.5349	Remote Similarity	NPC33619
0.5287	Remote Similarity	NPC81654
0.5185	Remote Similarity	NPC185200
0.5172	Remote Similarity	NPC483467
0.5114	Remote Similarity	NPC187106
0.51	Remote Similarity	NPC52254
0.51	Remote Similarity	NPC611036
0.5098	Remote Similarity	NPC486444
0.5098	Remote Similarity	NPC649
0.5062	Remote Similarity	NPC271797
0.506	Remote Similarity	NPC474897
0.5049	Remote Similarity	NPC199607
0.5049	Remote Similarity	NPC54591

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC523632 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	3206
0.1-0.2	5784
0.2-0.3	141
0.3-0.4	13
0.4-0.5	2
0.5-0.6	4
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
0.5517	Remote Similarity	NPD4500	Approved
0.5517	Remote Similarity	NPD4501	Approved
0.5349	Remote Similarity	NPD4601	Phase 4
0.5287	Remote Similarity	NPD4600	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