NPASS Compound

Natural Product: NPC611289

Natural Product ID	NPC611289
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	JBGBPOYDCGQCJC-MWKLXWFVSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL4473793
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 85 88 0 0 0 0 0 0 0 0999 V2000 4.2209 -1.5399 2.3391 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9555 -0.7590 2.1476 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8799 -1.3650 2.3441 O 0 0 0 0 0 0 0 0 0 0 0 0 2.9525 0.5524 1.7754 O 0 0 0 0 0 0 0 0 0 0 0 0 1.8273 1.3618 1.5668 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9811 0.8104 0.4472 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.1584 1.5576 0.2415 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.0731 0.7019 -0.3802 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.2843 1.3105 -0.6103 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.2907 0.6096 0.0308 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1787 0.6062 1.5369 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3210 -0.1850 2.0668 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.5348 0.4026 2.3189 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.6329 -0.2863 2.8150 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.4991 -1.6265 3.0669 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.5505 -2.4037 3.5680 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.2874 -2.2527 2.8232 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2026 -3.6334 3.1006 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.2163 -1.5398 2.3307 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4905 0.2578 -1.7471 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.1680 -1.0758 -1.5687 O 0 0 0 0 0 0 0 0 0 0 0 0 0.7372 1.1177 -2.0269 C 0 0 1 0 0 0 0 0 0 0 0 0 0.5786 2.3902 -2.0873 O 0 0 0 0 0 0 0 0 0 0 0 0 0.7069 3.4581 -2.7171 C 0 0 2 0 0 0 0 0 0 0 0 0 1.6552 4.4249 -2.2696 O 0 0 0 0 0 0 0 0 0 0 0 0 1.2233 5.0067 -1.0861 C 0 0 1 0 0 0 0 0 0 0 0 0 2.2937 5.8541 -0.4475 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0571 5.7898 -1.2903 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.4519 6.3754 -0.0921 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.1081 4.7865 -1.7738 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.2849 5.4982 -1.9275 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.5833 4.2432 -3.0851 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.2650 5.3533 -3.8683 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7502 0.8698 -0.8651 C 0 0 2 0 0 0 0 0 0 0 0 0 2.5890 -0.0725 -0.9840 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4960 -0.9595 -1.1189 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6156 -0.3314 -1.4048 O 0 0 0 0 0 0 0 0 0 0 0 0 3.5762 -2.3799 -1.0334 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6047 -3.2046 -0.7215 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7965 -4.6589 -0.6607 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9041 -5.3120 -1.0719 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0207 -6.6767 -0.8891 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9941 -7.4178 -0.2727 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1488 -8.7861 -0.1062 O 0 0 0 0 0 0 0 0 0 0 0 0 1.8692 -6.7594 0.1451 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8533 -7.5071 0.7604 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7657 -5.4101 -0.0427 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2079 -2.4975 1.7685 H 0 0 0 0 0 0 0 0 0 0 0 0 4.2885 -1.8159 3.4029 H 0 0 0 0 0 0 0 0 0 0 0 0 5.1039 -0.9802 2.0010 H 0 0 0 0 0 0 0 0 0 0 0 0 2.0868 2.4076 1.3804 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1673 1.3651 2.4825 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7580 -0.2532 0.6216 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2116 -0.1860 0.2396 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3015 0.9293 -0.2850 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1472 -0.4683 -0.2868 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2459 0.1755 1.9223 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2394 1.6432 1.9501 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.6528 1.4528 2.1224 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.5377 0.2464 2.9826 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.5157 -2.1850 3.3680 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.4898 -3.9945 4.0057 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2958 -2.0604 2.1552 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2960 0.3475 -2.4499 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9253 -1.6792 -1.7693 H 0 0 0 0 0 0 0 0 0 0 0 0 1.2133 0.6572 -2.8933 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1102 3.2732 -3.7773 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9771 4.1871 -0.3768 H 0 0 0 0 0 0 0 0 0 0 0 0 2.9827 6.2402 -1.2093 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8034 6.7094 0.1027 H 0 0 0 0 0 0 0 0 0 0 0 0 2.8761 5.2964 0.2883 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0871 6.6027 -2.0258 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4087 6.6312 -0.0950 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1831 4.0035 -1.0010 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2529 6.1626 -2.6402 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2889 3.6393 -3.6426 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2468 5.0975 -4.6721 H 0 0 0 0 0 0 0 0 0 0 0 0 2.2836 1.8899 -0.8534 H 0 0 0 0 0 0 0 0 0 0 0 0 4.5459 -2.8878 -1.2384 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6303 -2.8021 -0.5090 H 0 0 0 0 0 0 0 0 0 0 0 0 4.7165 -4.7631 -1.5570 H 0 0 0 0 0 0 0 0 0 0 0 0 4.8991 -7.2029 -1.2127 H 0 0 0 0 0 0 0 0 0 0 0 0 2.6999 -9.3212 0.6223 H 0 0 0 0 0 0 0 0 0 0 0 0 1.0783 -8.1623 1.5069 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8720 -4.8935 0.2959 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 2 0 2 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 1 0 10 11 1 0 11 12 1 0 12 13 2 0 13 14 1 0 14 15 2 0 15 16 1 0 15 17 1 0 17 18 1 0 17 19 2 0 8 20 1 0 20 21 1 0 20 22 1 0 22 23 1 0 23 24 1 0 24 25 1 0 25 26 1 0 26 27 1 0 26 28 1 0 28 29 1 0 28 30 1 0 30 31 1 0 30 32 1 0 32 33 1 0 22 34 1 0 34 35 1 0 35 36 1 0 36 37 2 0 36 38 1 0 38 39 2 0 39 40 1 0 40 41 2 0 41 42 1 0 42 43 2 0 43 44 1 0 43 45 1 0 45 46 1 0 45 47 2 0 34 6 1 0 47 40 1 0 19 12 1 0 32 24 1 0 1 48 1 0 1 49 1 0 1 50 1 0 5 51 1 0 5 52 1 0 6 53 1 1 8 54 1 1 10 55 1 0 10 56 1 0 11 57 1 0 11 58 1 0 13 59 1 0 14 60 1 0 16 61 1 0 18 62 1 0 19 63 1 0 20 64 1 6 21 65 1 0 22 66 1 6 24 67 1 6 26 68 1 1 27 69 1 0 27 70 1 0 27 71 1 0 28 72 1 6 29 73 1 0 30 74 1 1 31 75 1 0 32 76 1 6 33 77 1 0 34 78 1 1 38 79 1 0 39 80 1 0 41 81 1 0 42 82 1 0 44 83 1 0 46 84 1 0 47 85 1 0 M END

Standard InCHIKey	JBGBPOYDCGQCJC-MWKLXWFVSA-N
Standard InCHI	InChI=1S/C31H38O16/c1-14-24(38)25(39)26(40)31(44-14)47-29-27(41)30(42-10-9-17-4-7-19(34)21(36)12-17)45-22(13-43-15(2)32)28(29)46-23(37)8-5-16-3-6-18(33)20(35)11-16/h3-8,11-12,14,22,24-31,33-36,38-41H,9-10,13H2,1-2H3/b8-5+/t14-,22+,24-,25+,26+,27+,28+,29+,30+,31-/m0/s1
SMILES	CC(=O)OC[C@H]1O[C@@H](OCCc2ccc(O)c(O)c2)[C@H](O)[C@@H](O[C@@H]2O[C@@H](C)[C@H](O)[C@@H](O)[C@H]2O)[C@@H]1OC(=O)/C=C/c1ccc(O)c(O)c1

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
NPO56424	Tecoma mollis	Genus	Bignoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]

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

Activity Type	# Activity
IC50	1

Activity Type	# Activity
Individual protein	1

Molecular-level activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT325	Individual protein	Cyclooxygenase-2	Ovis aries	IC50	=	9400.0	nM	PMID[31255927]

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 NPC611289 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	14606
0.1-0.2	31220
0.2-0.3	3477
0.3-0.4	428
0.4-0.5	57
0.5-0.6	22
0.6-0.7	28
0.7-0.8	0
0.8-0.85	7
0.85-0.9	4
0.9-0.95	1
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.9091	High Similarity	NPC76406
0.8537	High Similarity	NPC205864
0.8537	High Similarity	NPC298257
0.8537	High Similarity	NPC247032
0.8537	High Similarity	NPC175214
0.8372	Intermediate Similarity	NPC106818
0.814	Intermediate Similarity	NPC300894
0.814	Intermediate Similarity	NPC23845
0.8125	Intermediate Similarity	NPC472350
0.8125	Intermediate Similarity	NPC197316
0.8125	Intermediate Similarity	NPC89105
0.8	Intermediate Similarity	NPC87403
0.7558	Intermediate Similarity	NPC269141
0.7317	Intermediate Similarity	NPC81515
0.7143	Intermediate Similarity	NPC64141
0.7097	Intermediate Similarity	NPC196063
0.7097	Intermediate Similarity	NPC604195
0.7079	Intermediate Similarity	NPC252292
0.7	Intermediate Similarity	NPC112
0.6989	Remote Similarity	NPC476384
0.6957	Remote Similarity	NPC259347
0.6923	Remote Similarity	NPC100998
0.6875	Remote Similarity	NPC64195
0.6824	Remote Similarity	NPC46137
0.6667	Remote Similarity	NPC483705
0.663	Remote Similarity	NPC119537
0.6598	Remote Similarity	NPC470933
0.6552	Remote Similarity	NPC483706
0.65	Remote Similarity	NPC229505
0.6495	Remote Similarity	NPC476380
0.6495	Remote Similarity	NPC476381
0.6404	Remote Similarity	NPC68092
0.6374	Remote Similarity	NPC263829
0.6364	Remote Similarity	NPC470934
0.6316	Remote Similarity	NPC96795
0.6316	Remote Similarity	NPC264632
0.6237	Remote Similarity	NPC34587
0.622	Remote Similarity	NPC287597
0.6211	Remote Similarity	NPC34927
0.618	Remote Similarity	NPC205195
0.6136	Remote Similarity	NPC260425
0.6122	Remote Similarity	NPC476375
0.6105	Remote Similarity	NPC296954
0.6058	Remote Similarity	NPC476386
0.6044	Remote Similarity	NPC134405
0.6023	Remote Similarity	NPC475530
0.602	Remote Similarity	NPC141455
0.5981	Remote Similarity	NPC257970
0.5979	Remote Similarity	NPC610636
0.5955	Remote Similarity	NPC235294
0.5833	Remote Similarity	NPC886
0.5814	Remote Similarity	NPC473285
0.5773	Remote Similarity	NPC476397
0.5698	Remote Similarity	NPC34293
0.5686	Remote Similarity	NPC476378
0.5579	Remote Similarity	NPC476377
0.5556	Remote Similarity	NPC473799
0.5521	Remote Similarity	NPC47471
0.5472	Remote Similarity	NPC94871
0.5455	Remote Similarity	NPC600370
0.5417	Remote Similarity	NPC476383
0.5405	Remote Similarity	NPC470927
0.5361	Remote Similarity	NPC106677
0.5234	Remote Similarity	NPC306890
0.5229	Remote Similarity	NPC188393
0.5155	Remote Similarity	NPC265648
0.5057	Remote Similarity	NPC288416
0.5052	Remote Similarity	NPC222433
0.5051	Remote Similarity	NPC476376

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC611289 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	5155
0.1-0.2	3916
0.2-0.3	77
0.3-0.4	1
0.4-0.5	0
0.5-0.6	0
0.6-0.7	0
0.7-0.8	0
0.8-0.85	1
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8125	Intermediate Similarity	NPD7266	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