NPASS Compound

Natural Product: NPC208463

Natural Product ID	NPC208463
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	GVUMSYCSEREXHD-RLWIGOAZSA-N
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 85 0 0 0 0 0 0 0 0999 V2000 -5.3731 -1.0728 -2.0642 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1332 0.1305 -1.1527 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.8621 1.2976 -1.7521 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6381 0.3456 -1.0852 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0557 -0.6107 -0.0688 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.5844 -0.5864 -0.1435 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0327 -0.9706 -1.2903 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4311 -1.0161 -1.5578 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0997 -0.1042 -0.5455 C 0 0 2 0 0 0 0 0 0 0 0 0 2.5286 0.1868 -0.7939 C 0 0 1 0 0 0 0 0 0 0 0 0 2.8871 -0.4901 -2.1017 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7440 1.6886 -1.0500 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0821 1.8382 -1.6794 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2119 1.3409 -0.8194 C 0 0 1 0 0 0 0 0 0 0 0 0 4.8726 0.3103 0.1856 C 0 0 0 0 0 0 0 0 0 0 0 0 5.4189 0.8501 1.5337 C 0 0 0 0 0 0 0 0 0 0 0 0 5.8426 -0.8729 -0.0501 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4821 -0.1574 0.3102 C 0 0 1 0 0 0 0 0 0 0 0 0 2.9548 0.2210 1.6614 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4880 0.4001 1.7848 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7023 -0.5200 0.8396 C 0 0 2 0 0 0 0 0 0 0 0 0 1.0731 -1.9049 1.2125 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7452 -0.1581 1.0279 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.9895 1.3006 1.2361 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3843 -0.9029 2.2015 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7976 -0.3608 2.4453 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.6592 -0.5268 1.2664 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.7559 0.5509 1.2230 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.7113 -0.1200 0.2253 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.5863 -1.5023 0.5341 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.5914 -1.7057 1.4763 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.4135 -2.5954 2.3257 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.8115 0.8781 3.0613 O 0 0 0 0 0 0 0 0 0 0 0 0 6.2571 0.9945 -1.6824 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.4234 -1.6043 -2.2900 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.8049 -0.7670 -3.0400 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.0191 -1.8254 -1.5520 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.9533 1.1458 -1.5159 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.5775 2.2668 -1.3436 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.7964 1.2291 -2.8591 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2290 0.0206 -2.0872 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3511 1.3836 -0.9806 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3265 -1.6270 -0.5102 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6695 -1.2878 -2.1297 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7017 -2.0810 -1.4561 H 0 0 0 0 0 0 0 0 0 0 0 0 0.5851 -0.6542 -2.5902 H 0 0 0 0 0 0 0 0 0 0 0 0 0.5338 0.8618 -0.7385 H 0 0 0 0 0 0 0 0 0 0 0 0 2.4831 -1.5185 -2.1944 H 0 0 0 0 0 0 0 0 0 0 0 0 2.4414 0.0914 -2.9633 H 0 0 0 0 0 0 0 0 0 0 0 0 3.9420 -0.5647 -2.3213 H 0 0 0 0 0 0 0 0 0 0 0 0 1.9796 2.0812 -1.7316 H 0 0 0 0 0 0 0 0 0 0 0 0 2.7558 2.1592 -0.0647 H 0 0 0 0 0 0 0 0 0 0 0 0 4.1349 1.4018 -2.7100 H 0 0 0 0 0 0 0 0 0 0 0 0 4.1810 2.9477 -1.9046 H 0 0 0 0 0 0 0 0 0 0 0 0 5.6278 2.2897 -0.3430 H 0 0 0 0 0 0 0 0 0 0 0 0 5.1665 0.2227 2.3754 H 0 0 0 0 0 0 0 0 0 0 0 0 6.5517 0.8303 1.4713 H 0 0 0 0 0 0 0 0 0 0 0 0 5.2166 1.9363 1.6350 H 0 0 0 0 0 0 0 0 0 0 0 0 6.8854 -0.5118 -0.0982 H 0 0 0 0 0 0 0 0 0 0 0 0 5.8234 -1.5097 0.8880 H 0 0 0 0 0 0 0 0 0 0 0 0 5.5208 -1.5392 -0.8414 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5118 -1.2909 0.3091 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2907 -0.5461 2.4204 H 0 0 0 0 0 0 0 0 0 0 0 0 3.4022 1.1794 2.0605 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1635 0.0676 2.8157 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1981 1.4426 1.7064 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2846 -2.5279 1.6610 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4682 -2.5316 0.3615 H 0 0 0 0 0 0 0 0 0 0 0 0 1.9153 -1.9682 1.9679 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0421 1.5474 0.9845 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4106 1.9915 0.6057 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7438 1.6243 2.2888 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6366 -1.9452 1.8351 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7700 -0.8983 3.0976 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1718 -1.0520 3.2682 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.3033 0.5912 2.1834 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4077 1.5126 0.8656 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.7319 0.2525 0.3335 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5518 0.9772 3.7111 H 0 0 0 0 0 0 0 0 0 0 0 0 6.2044 0.0409 -1.9252 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 2 4 1 0 4 5 1 0 5 6 1 0 6 7 2 0 7 8 1 0 8 9 1 0 9 10 1 0 10 11 1 6 10 12 1 0 12 13 1 0 13 14 1 0 14 15 1 0 15 16 1 0 15 17 1 0 15 18 1 0 18 19 1 0 19 20 1 0 20 21 1 0 21 22 1 1 21 23 1 0 23 24 1 1 23 25 1 0 25 26 1 0 26 27 1 0 27 28 1 0 28 29 1 0 29 30 1 0 30 31 1 0 31 32 2 0 26 33 1 0 14 34 1 0 29 2 1 0 27 5 1 0 23 6 1 0 27 31 1 1 21 9 1 0 18 10 1 0 1 35 1 0 1 36 1 0 1 37 1 0 3 38 1 0 3 39 1 0 3 40 1 0 4 41 1 0 4 42 1 0 5 43 1 6 7 44 1 0 8 45 1 0 8 46 1 0 9 47 1 6 11 48 1 0 11 49 1 0 11 50 1 0 12 51 1 0 12 52 1 0 13 53 1 0 13 54 1 0 14 55 1 1 16 56 1 0 16 57 1 0 16 58 1 0 17 59 1 0 17 60 1 0 17 61 1 0 18 62 1 1 19 63 1 0 19 64 1 0 20 65 1 0 20 66 1 0 22 67 1 0 22 68 1 0 22 69 1 0 24 70 1 0 24 71 1 0 24 72 1 0 25 73 1 0 25 74 1 0 26 75 1 1 28 76 1 0 28 77 1 0 29 78 1 6 33 79 1 0 34 80 1 0 M END

Standard InCHIKey	GVUMSYCSEREXHD-RLWIGOAZSA-N
Standard InCHI	InChI=1S/C30H46O4/c1-25(2)14-18-17-8-9-20-27(5)12-11-21(31)26(3,4)19(27)10-13-28(20,6)29(17,7)15-22(32)30(18)16-23(25)34-24(30)33/h8,18-23,31-32H,9-16H2,1-7H3/t18-,19+,20+,21-,22+,23-,27-,28+,29+,30+/m0/s1
SMILES	CC1(C)C[C@H]2C3=CC[C@@H]4[C@@]5(C)CC[C@@H](C(C)(C)[C@H]5CC[C@@]4(C)[C@]3(C)C[C@H]([C@]32C[C@@H]1OC3=O)O)O

Calculated Properties

Physi-Chem Properties

MedChem Properties

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

ADMET: Distribution

ADMET: Metabolism

ADMET: Excretion

ADMET: Toxicity

Species Source

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO12181	Albizia julibrissin	Species	Fabaceae	Eukaryota	n.a.	bark	n.a.	PMID[15283458]
NPO12181	Albizia julibrissin	Species	Fabaceae	Eukaryota	n.a.	stem	n.a.	PMID[15577257]
NPO12181	Albizia julibrissin	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[9051910]
NPO12181	Albizia julibrissin	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12181	Albizia julibrissin	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO12181	Albizia julibrissin	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO12181	Albizia julibrissin	Species	Fabaceae	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 NPC208463 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	18499
0.1-0.2	24674
0.2-0.3	5431
0.3-0.4	1040
0.4-0.5	158
0.5-0.6	40
0.6-0.7	6
0.7-0.8	0
0.8-0.85	0
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	NPC164349
0.7391	Intermediate Similarity	NPC488518
0.7015	Intermediate Similarity	NPC488519
0.6575	Remote Similarity	NPC283343
0.6571	Remote Similarity	NPC49776
0.6571	Remote Similarity	NPC63118
0.6571	Remote Similarity	NPC474436
0.6267	Remote Similarity	NPC473160
0.6164	Remote Similarity	NPC294360
0.597	Remote Similarity	NPC311078
0.597	Remote Similarity	NPC34177
0.5882	Remote Similarity	NPC253807
0.5882	Remote Similarity	NPC158662
0.5867	Remote Similarity	NPC488520
0.5857	Remote Similarity	NPC246708
0.5844	Remote Similarity	NPC258547
0.5797	Remote Similarity	NPC159168
0.5714	Remote Similarity	NPC471433
0.5714	Remote Similarity	NPC471432
0.5714	Remote Similarity	NPC488522
0.5699	Remote Similarity	NPC232237
0.5652	Remote Similarity	NPC235341
0.5638	Remote Similarity	NPC105800
0.557	Remote Similarity	NPC488524
0.5522	Remote Similarity	NPC290598
0.5522	Remote Similarity	NPC30590
0.5417	Remote Similarity	NPC488517
0.5395	Remote Similarity	NPC480919
0.5352	Remote Similarity	NPC470588
0.53	Remote Similarity	NPC207738
0.5286	Remote Similarity	NPC132478
0.5286	Remote Similarity	NPC101475
0.527	Remote Similarity	NPC2539
0.5248	Remote Similarity	NPC210729
0.5248	Remote Similarity	NPC82931
0.5205	Remote Similarity	NPC40552
0.52	Remote Similarity	NPC7260
0.52	Remote Similarity	NPC210037
0.52	Remote Similarity	NPC120968
0.52	Remote Similarity	NPC227467
0.52	Remote Similarity	NPC273621
0.5196	Remote Similarity	NPC172365
0.519	Remote Similarity	NPC475263
0.5125	Remote Similarity	NPC273668
0.5072	Remote Similarity	NPC27765
0.5072	Remote Similarity	NPC120098
0.5072	Remote Similarity	NPC122418
0.5072	Remote Similarity	NPC491014
0.5068	Remote Similarity	NPC480950

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC208463 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6820
0.1-0.2	2246
0.2-0.3	79
0.3-0.4	4
0.4-0.5	0
0.5-0.6	1
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
0.52	Remote Similarity	NPD7645	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