NPASS Compound

Natural Product: NPC490674

Natural Product ID	NPC490674
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	11-oxo-Î²-amyrin
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	n.a.
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001553] Triterpenoids

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 80 84 0 0 0 0 0 0 0 0999 V2000 -3.0196 0.1190 0.1612 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9472 -1.0351 0.1171 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.3112 -0.7154 -0.4534 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0168 -2.0793 -0.5555 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.1702 0.1023 0.4702 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1894 -0.1823 -1.8308 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8996 0.4879 -2.1598 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2060 1.1088 -0.9675 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.0290 2.2999 -0.5437 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8833 1.6009 -1.4832 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8208 1.9052 -0.4834 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6783 0.8659 0.6157 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3878 1.4626 1.8479 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5711 -0.2260 0.1438 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0542 -1.3427 -0.2595 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4006 -1.5980 -0.2471 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8156 -2.7572 -0.3888 O 0 0 0 0 0 0 0 0 0 0 0 0 1.3124 -0.4482 -0.0669 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7418 -0.7866 0.1012 C 0 0 1 0 0 0 0 0 0 0 0 0 2.8323 -2.1622 0.7335 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2643 -1.0108 -1.3350 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6961 -1.4099 -1.3583 C 0 0 0 0 0 0 0 0 0 0 0 0 5.5786 -0.4707 -0.6220 C 0 0 2 0 0 0 0 0 0 0 0 0 6.5003 -1.1564 0.1869 O 0 0 0 0 0 0 0 0 0 0 0 0 4.8545 0.6202 0.1223 C 0 0 0 0 0 0 0 0 0 0 0 0 5.8674 1.0801 1.1918 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6540 1.7911 -0.7658 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6110 0.1479 0.8526 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9773 1.3140 1.5061 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6017 1.6548 1.0507 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7013 0.4561 0.9657 C 0 0 1 0 0 0 0 0 0 0 0 0 0.6758 -0.2184 2.3224 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2542 0.6688 1.0971 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1508 -1.4229 1.1612 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6024 -1.9250 -0.4418 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.3051 -2.8615 -0.8484 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.5613 -2.2958 0.3791 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.7605 -1.9672 -1.3687 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.5977 0.9866 -0.0742 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.5666 0.4156 1.3475 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.0468 -0.4387 0.8809 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.3906 -0.9922 -2.5600 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.0439 0.5438 -1.9800 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2314 -0.2319 -2.6747 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.0951 1.3078 -2.8809 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.9739 2.4008 -1.1533 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4987 3.2612 -0.7057 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.2697 2.2614 0.5285 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5393 0.9301 -2.3012 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1033 2.5721 -2.0098 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0305 2.9043 -0.0482 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1101 2.0295 -1.0778 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1211 2.2351 1.5376 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6579 2.0428 2.4633 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7993 0.6821 2.5084 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6648 -2.1473 -0.6292 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1803 0.1434 -1.0365 H 0 0 0 0 0 0 0 0 0 0 0 0 3.0325 -2.9804 0.0176 H 0 0 0 0 0 0 0 0 0 0 0 0 3.7742 -2.1710 1.3848 H 0 0 0 0 0 0 0 0 0 0 0 0 2.0377 -2.3711 1.4727 H 0 0 0 0 0 0 0 0 0 0 0 0 2.6768 -1.9172 -1.6757 H 0 0 0 0 0 0 0 0 0 0 0 0 2.9759 -0.2148 -2.0166 H 0 0 0 0 0 0 0 0 0 0 0 0 4.8056 -2.4330 -0.8978 H 0 0 0 0 0 0 0 0 0 0 0 0 4.9826 -1.5461 -2.4184 H 0 0 0 0 0 0 0 0 0 0 0 0 6.2183 0.0577 -1.3886 H 0 0 0 0 0 0 0 0 0 0 0 0 6.7430 -1.9782 -0.3219 H 0 0 0 0 0 0 0 0 0 0 0 0 6.3220 0.1397 1.5903 H 0 0 0 0 0 0 0 0 0 0 0 0 6.6655 1.6641 0.7089 H 0 0 0 0 0 0 0 0 0 0 0 0 5.3635 1.5841 2.0144 H 0 0 0 0 0 0 0 0 0 0 0 0 4.9046 2.7716 -0.2628 H 0 0 0 0 0 0 0 0 0 0 0 0 3.6839 1.9250 -1.2243 H 0 0 0 0 0 0 0 0 0 0 0 0 5.4003 1.7397 -1.6125 H 0 0 0 0 0 0 0 0 0 0 0 0 4.0726 -0.4394 1.7145 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5786 2.2631 1.3520 H 0 0 0 0 0 0 0 0 0 0 0 0 2.9249 1.2454 2.6356 H 0 0 0 0 0 0 0 0 0 0 0 0 1.2130 2.4268 1.7686 H 0 0 0 0 0 0 0 0 0 0 0 0 1.7130 2.2061 0.0980 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6957 -0.3806 2.7243 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1529 0.3890 3.0590 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1368 -1.1967 2.2960 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 3 5 1 0 3 6 1 0 6 7 1 0 7 8 1 0 8 9 1 1 8 10 1 0 10 11 1 0 11 12 1 0 12 13 1 0 12 14 1 0 14 15 2 0 15 16 1 0 16 17 2 0 16 18 1 0 18 19 1 0 19 20 1 1 19 21 1 0 21 22 1 0 22 23 1 0 23 24 1 0 23 25 1 0 25 26 1 0 25 27 1 0 25 28 1 0 28 29 1 0 29 30 1 0 30 31 1 0 31 32 1 1 8 1 1 0 31 12 1 0 14 1 1 0 31 18 1 0 28 19 1 0 1 33 1 0 2 34 1 0 2 35 1 0 4 36 1 0 4 37 1 0 4 38 1 0 5 39 1 0 5 40 1 0 5 41 1 0 6 42 1 0 6 43 1 0 7 44 1 0 7 45 1 0 9 46 1 0 9 47 1 0 9 48 1 0 10 49 1 0 10 50 1 0 11 51 1 0 11 52 1 0 13 53 1 0 13 54 1 0 13 55 1 0 15 56 1 0 18 57 1 0 20 58 1 0 20 59 1 0 20 60 1 0 21 61 1 0 21 62 1 0 22 63 1 0 22 64 1 0 23 65 1 6 24 66 1 0 26 67 1 0 26 68 1 0 26 69 1 0 27 70 1 0 27 71 1 0 27 72 1 0 28 73 1 0 29 74 1 0 29 75 1 0 30 76 1 0 30 77 1 0 32 78 1 0 32 79 1 0 32 80 1 0 M END

Standard InCHIKey	UKAIYBGRLWQHDQ-ACHYJBJUSA-N
Standard InCHI	InChI=1S/C30H48O2/c1-25(2)13-14-27(5)15-16-29(7)19(20(27)18-25)17-21(31)24-28(6)11-10-23(32)26(3,4)22(28)9-12-30(24,29)8/h17,20,22-24,32H,9-16,18H2,1-8H3/t20?,22?,23-,24?,27+,28-,29?,30+/m0/s1
SMILES	[H]C12CC(C)(C)CC[C@]1(C)CCC1(C)C2=CC(=O)C2[C@@]3(C)CC[C@H](O)C(C)(C)C3CC[C@]21C

Calculated Properties

Physi-Chem Properties

Molecular Weight:	440.37	Volume:	496.961 ? Van der Waals volume.
Dense:	0.886	LogP:	4.43 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	4.057 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-5.359 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	0.0	Rigid Bonds:	27.0
TPSA:	37.3 ? Topological Polar Surface Area.	H-Bond Acceptor:	2.0
H-Bond Donor:	1.0	Rings:	5.0
Heavy Atoms:	2.0

MedChem Properties

QED Drug-Likeness Score:	0.427	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	4.632	Fsp³:	0.9
MCE-18:	104.0 ? MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.	Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted	GSK Rule:	Accepted
Golden Triangle Rule:	Rejected	BMS Rule:	0
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.52	Fluc inhibitor:	0.0 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.03 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.019 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.426	Promiscuous compounds:	0.23

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.145	MDCK Permeability:	-4.888
Pgp-inhibitor:	0.923	Pgp-substrate:	0.105
PAMPA:	0.849 ? 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%):	0.547	30% Bioavailability (F30%):	0.074
50% Bioavailability (F50%):	0.994

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.962	MRP1:	0.992
Plasma Protein Binding (PPB):	97.609%	Volume Distribution (VD):	0.046
Fu:	2.792% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	1.0
OATP1B3 inhibitor:	0.989	BCRP inhibitor:	0.164
BSEP inhibitor:	0.998

ADMET: Metabolism

CYP1A2-inhibitor:	0.018	CYP1A2-substrate:	0.955
CYP2C19-inhibitor:	1.0	CYP2C19-substrate:	0.935
CYP2C9-inhibitor:	0.651	CYP2C9-substrate:	0.01
CYP2D6-inhibitor:	0.299	CYP2D6-substrate:	0.11
CYP3A4-inhibitor:	0.988	CYP3A4-substrate:	0.001
CYP2B6-substrate:	0.502	CYP2C8-inhibitor:	0.165
HLM stability:	0.998 ? 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):

10.347

Half-life (T1/2):

0.178

ADMET: Toxicity

hERG Blockers:	0.077	hERG Blockers (10um):	0.424
Human Hepatotoxicity (H-HT):	0.813	Drug-induced Liver Injury (DILI):	0.099
AMES Toxicity:	0.254	Rat Oral Acute Toxicity:	0.488
Maximum Recommended Daily Dose:	0.83	Skin Sensitization:	0.522
Carcinogencity:	0.928	Eye Corrosion:	0.025
Eye Irritation:	0.693	Respiratory Toxicity:	0.819
Drug-induced Neurotoxicity:	0.162	Ototoxicity:	0.609
Hematotoxicity:	0.129	Drug-induced Nephrotoxicity:	0.325
Genotoxicity:	0.162	RPMI-8226 Immunitoxicity:	0.054
A549 Cytotoxicity:	0.277	Hek293 Cytotoxicity:	0.589
BCF:	2.749 ? 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:	5.145 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	6.422 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	6.314 ? 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
NPO41948	A new engineered strain of Nicotiana benthamiana [TS gene]	Strain	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24463610]

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 NPC490674 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	18279
0.1-0.2	25581
0.2-0.3	5175
0.3-0.4	655
0.4-0.5	137
0.5-0.6	8
0.6-0.7	9
0.7-0.8	1
0.8-0.85	1
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.8103	Intermediate Similarity	NPC214756
0.7797	Intermediate Similarity	NPC295643
0.7414	Intermediate Similarity	NPC602872
0.7031	Intermediate Similarity	NPC4036
0.7031	Intermediate Similarity	NPC65120
0.7031	Intermediate Similarity	NPC145067
0.7031	Intermediate Similarity	NPC233455
0.7031	Intermediate Similarity	NPC158030
0.7018	Intermediate Similarity	NPC190035
0.6721	Remote Similarity	NPC480944
0.6552	Remote Similarity	NPC290598
0.6552	Remote Similarity	NPC30590
0.6508	Remote Similarity	NPC479748
0.6406	Remote Similarity	NPC272075
0.6324	Remote Similarity	NPC471966
0.6129	Remote Similarity	NPC475862
0.6119	Remote Similarity	NPC98874
0.6032	Remote Similarity	NPC470588
0.5873	Remote Similarity	NPC235341
0.5797	Remote Similarity	NPC610635
0.5606	Remote Similarity	NPC246708
0.5469	Remote Similarity	NPC101475
0.5469	Remote Similarity	NPC196753
0.5312	Remote Similarity	NPC474989
0.5224	Remote Similarity	NPC73969
0.5143	Remote Similarity	NPC488519

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC490674 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6781
0.1-0.2	2213
0.2-0.3	148
0.3-0.4	1
0.4-0.5	6
0.5-0.6	0
0.6-0.7	0
0.7-0.8	1
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
0.7031	Intermediate Similarity	NPD7515	Phase 2

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