NPASS Compound

Natural Product: NPC62418

Natural Product ID	NPC62418
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	HBPNZWWAQVKYPJ-MDLURYLBSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	21586699
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000279] Alkaloids and derivatives [CHEMONTID:0001786] Yohimbine alkaloids

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 51 55 0 0 0 0 0 0 0 0999 V2000 -3.2084 -3.4963 0.9902 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0644 -2.3851 -0.0181 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.7593 -1.6886 0.0328 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.3909 -1.1192 1.3621 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0247 -0.6523 1.2911 N 0 0 0 0 0 0 0 0 0 0 0 0 0.9257 -1.7415 1.2681 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2180 -1.1412 1.8432 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6149 -0.1249 0.8349 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8418 0.3337 0.3920 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1496 0.0166 0.7250 C 0 0 0 0 0 0 0 0 0 0 0 0 6.2365 0.6186 0.1370 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0093 1.5774 -0.8237 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7208 1.9150 -1.1768 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6366 1.3044 -0.5802 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3067 1.4253 -0.7174 N 0 0 0 0 0 0 0 0 0 0 0 0 1.6560 0.5691 0.1299 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1918 0.3634 0.3194 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.4186 -0.0060 -1.0052 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.8225 -0.5136 -0.9370 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.8653 0.3840 -0.4896 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9562 -0.1581 0.0235 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1581 -1.5127 0.1552 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.8293 1.8388 -0.5648 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9014 2.5312 -1.0170 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.9122 2.6002 -0.1006 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.9341 4.0153 -0.1478 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1594 0.8848 -2.0219 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.2966 -4.0870 1.1300 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5878 -3.0743 1.9432 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.0030 -4.1783 0.6194 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1726 -2.8497 -1.0224 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9410 -2.3937 -0.2583 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0108 -0.2529 1.6683 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4368 -1.8511 2.1968 H 0 0 0 0 0 0 0 0 0 0 0 0 0.5582 -2.5749 1.8603 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1417 -1.9723 0.2094 H 0 0 0 0 0 0 0 0 0 0 0 0 2.0162 -0.6088 2.7966 H 0 0 0 0 0 0 0 0 0 0 0 0 2.9818 -1.9281 1.9753 H 0 0 0 0 0 0 0 0 0 0 0 0 5.2622 -0.7557 1.4979 H 0 0 0 0 0 0 0 0 0 0 0 0 7.2448 0.3536 0.4143 H 0 0 0 0 0 0 0 0 0 0 0 0 6.8789 2.0585 -1.2935 H 0 0 0 0 0 0 0 0 0 0 0 0 4.5971 2.6734 -1.9361 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8780 2.0944 -1.3912 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1881 1.3389 0.7015 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1807 -0.9297 -1.3120 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0313 -0.9832 -1.9301 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.7772 0.4930 0.3785 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.0221 4.3049 -0.1596 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4514 4.3958 -1.0690 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5025 4.4213 0.7777 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4215 0.4678 -2.8673 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 3 4 1 0 4 5 1 0 5 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 2 0 12 13 1 0 13 14 2 0 14 15 1 0 15 16 1 0 16 17 1 0 17 18 1 0 18 19 1 0 19 20 1 0 20 21 2 0 21 22 1 0 20 23 1 0 23 24 2 0 23 25 1 0 25 26 1 0 18 27 1 0 22 2 1 0 19 3 1 0 17 5 1 0 16 8 2 0 14 9 1 0 1 28 1 0 1 29 1 0 1 30 1 0 2 31 1 6 3 32 1 6 4 33 1 0 4 34 1 0 6 35 1 0 6 36 1 0 7 37 1 0 7 38 1 0 10 39 1 0 11 40 1 0 12 41 1 0 13 42 1 0 15 43 1 0 17 44 1 1 18 45 1 6 19 46 1 6 21 47 1 0 26 48 1 0 26 49 1 0 26 50 1 0 27 51 1 0 M END

Standard InCHIKey	HBPNZWWAQVKYPJ-MDLURYLBSA-N
Standard InCHI	InChI=1S/C21H24N2O4/c1-11-14-9-23-8-7-13-12-5-3-4-6-16(12)22-18(13)19(23)20(24)17(14)15(10-27-11)21(25)26-2/h3-6,10-11,14,17,19-20,22,24H,7-9H2,1-2H3/t11-,14+,17+,19+,20-/m1/s1
SMILES	C[C@@H]1[C@@H]2CN3CCc4c5ccccc5[nH]c4[C@H]3[C@@H]([C@@H]2C(=CO1)C(=O)OC)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	368.17	Volume:	370.326 ? Van der Waals volume.
Dense:	0.994	LogP:	2.056 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	2.291 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-3.619 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	2.0	Rigid Bonds:	26.0
TPSA:	74.79 ? Topological Polar Surface Area.	H-Bond Acceptor:	6.0
H-Bond Donor:	2.0	Rings:	5.0
Heavy Atoms:	6.0

MedChem Properties

QED Drug-Likeness Score:	0.755	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	4.266	Fsp³:	0.476
MCE-18:	94.935 ? 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:	0.468	Fluc inhibitor:	0.059 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.663 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.18 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.002	Promiscuous compounds:	0.235

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.62	MDCK Permeability:	-4.982
Pgp-inhibitor:	0.001	Pgp-substrate:	0.402
PAMPA:	0.615 ? 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%):	0.418	30% Bioavailability (F30%):	0.759
50% Bioavailability (F50%):	0.993

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.916	MRP1:	0.998
Plasma Protein Binding (PPB):	68.483%	Volume Distribution (VD):	0.305
Fu:	30.313% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.958
OATP1B3 inhibitor:	0.99	BCRP inhibitor:	0.465
BSEP inhibitor:	0.939

ADMET: Metabolism

CYP1A2-inhibitor:	0.874	CYP1A2-substrate:	0.523
CYP2C19-inhibitor:	0.642	CYP2C19-substrate:	0.113
CYP2C9-inhibitor:	0.0	CYP2C9-substrate:	0.985
CYP2D6-inhibitor:	0.001	CYP2D6-substrate:	0.054
CYP3A4-inhibitor:	0.999	CYP3A4-substrate:	1.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.993
HLM stability:	0.976 ? 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):

7.559

Half-life (T1/2):

1.665

ADMET: Toxicity

hERG Blockers:	0.231	hERG Blockers (10um):	0.518
Human Hepatotoxicity (H-HT):	0.444	Drug-induced Liver Injury (DILI):	0.602
AMES Toxicity:	0.868	Rat Oral Acute Toxicity:	0.706
Maximum Recommended Daily Dose:	0.82	Skin Sensitization:	0.993
Carcinogencity:	0.808	Eye Corrosion:	0.0
Eye Irritation:	0.342	Respiratory Toxicity:	0.919
Drug-induced Neurotoxicity:	0.768	Ototoxicity:	0.627
Hematotoxicity:	0.57	Drug-induced Nephrotoxicity:	0.89
Genotoxicity:	0.956	RPMI-8226 Immunitoxicity:	0.107
A549 Cytotoxicity:	0.647	Hek293 Cytotoxicity:	0.659
BCF:	0.623 ? 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:	3.319 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	4.778 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.179 ? 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
NPO22126	Penicillium funiculosum	Species	Trichocomaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[27359163]
NPO10315	Cestrum parqui	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO22126	Penicillium funiculosum	Species	Trichocomaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO14694	Sickingia williamsii	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[COCONUT]
NPO1603	Monostroma nitidum	Species	Monostromataceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO1603	Monostroma nitidum	Species	Monostromataceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO10315	Cestrum parqui	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10499	Haplopappus paucidentatus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11596	Lomatia ilicifolia	Species	Proteaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19160	Klasea quinquefolia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6849	Lomatia arborescens	Species	Proteaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22126	Penicillium funiculosum	Species	Trichocomaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14694	Sickingia williamsii	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO907	Dictyostelium purpureum	Species	n.a.	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9282	Stereocaulon colensoi	Species	Stereocaulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4468	Cuspidaria pterocarpa	Species	Bignoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1603	Monostroma nitidum	Species	Monostromataceae	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 NPC62418 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	15129
0.1-0.2	33530
0.2-0.3	945
0.3-0.4	191
0.4-0.5	36
0.5-0.6	22
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	Natural Product ID
0.716	Intermediate Similarity	NPC312870
0.716	Intermediate Similarity	NPC199851
0.716	Intermediate Similarity	NPC294909
0.716	Intermediate Similarity	NPC254240
0.716	Intermediate Similarity	NPC128265
0.716	Intermediate Similarity	NPC604675
0.5814	Remote Similarity	NPC486449
0.5814	Remote Similarity	NPC63199
0.5814	Remote Similarity	NPC111602
0.5814	Remote Similarity	NPC102338
0.5814	Remote Similarity	NPC196251
0.5667	Remote Similarity	NPC603895
0.5632	Remote Similarity	NPC273374
0.5604	Remote Similarity	NPC21638
0.5568	Remote Similarity	NPC107782
0.5568	Remote Similarity	NPC486454
0.5281	Remote Similarity	NPC486443
0.5281	Remote Similarity	NPC486446
0.5169	Remote Similarity	NPC486452
0.5169	Remote Similarity	NPC74591
0.5111	Remote Similarity	NPC313985
0.5111	Remote Similarity	NPC249150
0.5111	Remote Similarity	NPC33619
0.5056	Remote Similarity	NPC220151
0.5056	Remote Similarity	NPC19692
0.5055	Remote Similarity	NPC81654
0.5055	Remote Similarity	NPC175474
0.5055	Remote Similarity	NPC99921

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC62418 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	3636
0.1-0.2	5350
0.2-0.3	146
0.3-0.4	12
0.4-0.5	2
0.5-0.6	2
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
0.716	Intermediate Similarity	NPD4500	Approved
0.716	Intermediate Similarity	NPD4501	Approved
0.5111	Remote Similarity	NPD4601	Phase 4
0.5055	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