NPASS Compound

Natural Product: NPC293026

Natural Product ID	NPC293026
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	VOQBIBADLOXXDT-MRYCCUBWSA-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:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0000337] Flavans [CHEMONTID:0003012] Flavan-3-ols [CHEMONTID:0001584] Catechins

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 67 72 0 0 0 0 0 0 0 0999 V2000 -4.0204 -1.8614 0.6768 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.5236 -2.9630 1.3852 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7157 -4.0241 1.6971 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4012 -4.0216 1.3190 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9177 -2.9234 0.6182 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7128 -1.8487 0.2960 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1285 -0.7233 -0.4310 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.9003 0.5106 -0.5756 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.3545 1.2713 0.5960 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.4925 2.0672 -0.0121 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1492 3.2239 0.3383 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.1916 3.7180 -0.4550 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.5754 3.0580 -1.5939 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9249 1.9038 -1.9495 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9066 1.4302 -1.1655 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1045 0.3009 -1.3087 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.6283 3.5759 -2.3761 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.8006 3.9178 1.4674 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.6747 -0.5177 -0.0976 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3150 -0.2249 1.1841 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0279 -0.0163 1.4918 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9838 -0.1059 0.5085 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6346 -0.4017 -0.7913 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6050 -0.5181 -1.9140 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0055 -0.6229 -1.3529 C 0 0 1 0 0 0 0 0 0 0 0 0 4.1394 0.4752 -0.3234 C 0 0 2 0 0 0 0 0 0 0 0 0 5.5491 0.7049 0.0639 C 0 0 0 0 0 0 0 0 0 0 0 0 6.1902 1.8312 -0.4241 C 0 0 0 0 0 0 0 0 0 0 0 0 7.5027 2.1304 -0.1190 C 0 0 0 0 0 0 0 0 0 0 0 0 8.2276 1.2857 0.7062 C 0 0 0 0 0 0 0 0 0 0 0 0 7.5776 0.1675 1.1856 C 0 0 0 0 0 0 0 0 0 0 0 0 6.2593 -0.1245 0.8735 C 0 0 0 0 0 0 0 0 0 0 0 0 8.2960 -0.6881 2.0153 O 0 0 0 0 0 0 0 0 0 0 0 0 9.5619 1.5646 1.0330 O 0 0 0 0 0 0 0 0 0 0 0 0 3.3352 0.0950 0.7728 O 0 0 0 0 0 0 0 0 0 0 0 0 4.1985 -1.8816 -0.7877 O 0 0 0 0 0 0 0 0 0 0 0 0 0.3166 -0.6043 -1.0839 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0668 -0.9073 -2.4015 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.2777 -0.1345 2.1873 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.6030 -5.1095 1.6471 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.2103 -5.1295 2.4050 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.7142 -1.0618 0.4547 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.5511 -2.9745 1.6857 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8700 -2.9327 0.3227 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0596 -1.1341 -1.5163 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3099 1.2198 -1.2518 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6767 0.7511 1.4855 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6261 2.0664 0.9327 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.7162 4.6253 -0.1918 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.2150 1.3598 -2.8559 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.4263 4.3635 -2.9747 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.9553 3.5679 2.3955 H 0 0 0 0 0 0 0 0 0 0 0 0 1.3298 0.2136 2.4850 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5269 0.4440 -2.4865 H 0 0 0 0 0 0 0 0 0 0 0 0 2.3403 -1.3853 -2.5506 H 0 0 0 0 0 0 0 0 0 0 0 0 4.7417 -0.4637 -2.1476 H 0 0 0 0 0 0 0 0 0 0 0 0 3.7023 1.3944 -0.7609 H 0 0 0 0 0 0 0 0 0 0 0 0 5.6380 2.5184 -1.0811 H 0 0 0 0 0 0 0 0 0 0 0 0 7.9967 3.0087 -0.5018 H 0 0 0 0 0 0 0 0 0 0 0 0 5.7626 -1.0127 1.2618 H 0 0 0 0 0 0 0 0 0 0 0 0 9.0802 -0.3374 2.5547 H 0 0 0 0 0 0 0 0 0 0 0 0 10.1968 1.8564 0.2854 H 0 0 0 0 0 0 0 0 0 0 0 0 3.8389 -1.9247 0.1533 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3982 -0.3421 -3.1278 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0343 0.3313 3.0631 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7708 -6.0310 1.2166 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4421 -6.0004 1.9304 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 2 3 1 0 3 4 2 0 4 5 1 0 5 6 2 0 6 7 1 0 7 8 1 0 8 9 1 0 9 10 1 0 10 11 2 0 11 12 1 0 12 13 2 0 13 14 1 0 14 15 2 0 15 16 1 0 13 17 1 0 11 18 1 0 7 19 1 0 19 20 2 0 20 21 1 0 21 22 2 0 22 23 1 0 23 24 1 0 24 25 1 0 25 26 1 0 26 27 1 0 27 28 2 0 28 29 1 0 29 30 2 0 30 31 1 0 31 32 2 0 31 33 1 0 30 34 1 0 26 35 1 0 25 36 1 0 23 37 2 0 37 38 1 0 20 39 1 0 4 40 1 0 3 41 1 0 6 1 1 0 16 8 1 0 37 19 1 0 15 10 1 0 35 22 1 0 32 27 1 0 1 42 1 0 2 43 1 0 5 44 1 0 7 45 1 6 8 46 1 6 9 47 1 0 9 48 1 0 12 49 1 0 14 50 1 0 17 51 1 0 18 52 1 0 21 53 1 0 24 54 1 0 24 55 1 0 25 56 1 6 26 57 1 6 28 58 1 0 29 59 1 0 32 60 1 0 33 61 1 0 34 62 1 0 36 63 1 0 38 64 1 0 39 65 1 0 40 66 1 0 41 67 1 0 M END

Standard InCHIKey	VOQBIBADLOXXDT-MRYCCUBWSA-N
Standard InCHI	InChI=1S/C30H26O11/c31-14-7-19(34)15-10-26(40-24(15)8-14)27(12-1-3-17(32)20(35)5-12)28-22(37)11-25-16(29(28)39)9-23(38)30(41-25)13-2-4-18(33)21(36)6-13/h1-8,11,23,26-27,30-39H,9-10H2/t23-,26-,27-,30-/m0/s1
SMILES	c1cc(c(cc1[C@@H]([C@@H]1Cc2c(cc(cc2O1)O)O)c1c(cc2c(C[C@@H]([C@H](c3ccc(c(c3)O)O)O2)O)c1O)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
NPO9390	Uncaria gambir	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21192716]
NPO9390	Uncaria gambir	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO9390	Uncaria gambir	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO9390	Uncaria gambir	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO9390	Uncaria gambir	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO9390	Uncaria gambir	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 NPC293026 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	23121
0.1-0.2	23958
0.2-0.3	2489
0.3-0.4	148
0.4-0.5	102
0.5-0.6	25
0.6-0.7	12
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	Natural Product ID
0.7606	Intermediate Similarity	NPC302549
0.662	Remote Similarity	NPC294558
0.662	Remote Similarity	NPC18185
0.662	Remote Similarity	NPC263940
0.6508	Remote Similarity	NPC261619
0.6508	Remote Similarity	NPC61477
0.6508	Remote Similarity	NPC78770
0.6508	Remote Similarity	NPC219876
0.6508	Remote Similarity	NPC126029
0.6508	Remote Similarity	NPC15658
0.6184	Remote Similarity	NPC226809
0.6027	Remote Similarity	NPC82917
0.6026	Remote Similarity	NPC601612
0.56	Remote Similarity	NPC58190
0.56	Remote Similarity	NPC108811
0.56	Remote Similarity	NPC170103
0.56	Remote Similarity	NPC236202
0.56	Remote Similarity	NPC262911
0.56	Remote Similarity	NPC202742
0.5526	Remote Similarity	NPC246202
0.5526	Remote Similarity	NPC224161
0.5526	Remote Similarity	NPC46335
0.5526	Remote Similarity	NPC279406
0.5526	Remote Similarity	NPC486519
0.5455	Remote Similarity	NPC207179
0.5455	Remote Similarity	NPC167571
0.5455	Remote Similarity	NPC278552
0.5443	Remote Similarity	NPC610767
0.5341	Remote Similarity	NPC478340
0.5244	Remote Similarity	NPC278548
0.5224	Remote Similarity	NPC268266
0.5224	Remote Similarity	NPC42760
0.5224	Remote Similarity	NPC220825
0.5224	Remote Similarity	NPC268342
0.519	Remote Similarity	NPC28440
0.5063	Remote Similarity	NPC184245
0.5063	Remote Similarity	NPC187801
0.5063	Remote Similarity	NPC610920

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC293026 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4702
0.1-0.2	4362
0.2-0.3	78
0.3-0.4	6
0.4-0.5	0
0.5-0.6	0
0.6-0.7	2
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
0.6508	Remote Similarity	NPD1612	Clinical (unspecified phase)
0.6508	Remote Similarity	NPD1613	Phase 4

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