NPASS Compound

Natural Product: NPC610635

Natural Product ID	NPC610635
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	MDQJVSLVPQYJLP-HUWCOUCRSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL603710
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 80 84 0 0 0 0 0 0 0 0999 V2000 3.3352 2.7184 1.0524 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4547 1.4150 0.2123 C 0 0 1 0 0 0 0 0 0 0 0 0 4.8615 1.4096 -0.2802 C 0 0 2 0 0 0 0 0 0 0 0 0 4.9820 1.2294 -1.7780 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6701 0.4167 0.4909 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1167 -0.9612 0.3383 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6852 -1.0707 0.8376 C 0 0 2 0 0 0 0 0 0 0 0 0 3.8333 -1.6578 2.2276 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3377 -2.7328 2.5846 O 0 0 0 0 0 0 0 0 0 0 0 0 4.5749 -0.9212 3.1301 O 0 0 0 0 0 0 0 0 0 0 0 0 3.0317 -2.1265 0.0276 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5285 -2.2093 0.1137 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9412 -0.7932 -0.1709 C 0 0 2 0 0 0 0 0 0 0 0 0 1.5379 -0.5034 -1.5346 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5410 -0.0168 0.9177 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8125 0.4758 1.8753 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6276 0.2507 1.8617 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2618 0.1444 2.9419 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.2205 0.1673 0.5299 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.7322 0.1187 0.5577 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.3217 -0.9663 1.3624 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1443 1.4285 1.2676 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3260 2.0734 0.6495 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.3201 1.1746 0.0025 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.0566 0.4011 0.9101 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.6661 0.3469 -1.0687 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.3733 -0.9441 -1.1909 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.8673 1.1118 -2.3910 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1889 0.2875 -0.8524 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.4858 -0.5456 -1.8701 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9686 -0.3582 -1.7615 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5215 -0.7893 -0.3359 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.9937 -2.2222 -0.2575 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0042 0.2341 0.9956 C 0 0 2 0 0 0 0 0 0 0 0 0 4.0355 2.6615 1.9146 H 0 0 0 0 0 0 0 0 0 0 0 0 3.7220 3.5259 0.3940 H 0 0 0 0 0 0 0 0 0 0 0 0 2.2940 2.8655 1.3675 H 0 0 0 0 0 0 0 0 0 0 0 0 2.7624 1.7008 -0.6381 H 0 0 0 0 0 0 0 0 0 0 0 0 5.3873 2.3994 -0.1041 H 0 0 0 0 0 0 0 0 0 0 0 0 4.8851 0.2021 -2.1233 H 0 0 0 0 0 0 0 0 0 0 0 0 5.9005 1.6734 -2.1873 H 0 0 0 0 0 0 0 0 0 0 0 0 4.1305 1.8177 -2.2265 H 0 0 0 0 0 0 0 0 0 0 0 0 6.6953 0.4149 0.0670 H 0 0 0 0 0 0 0 0 0 0 0 0 5.6762 0.7447 1.5550 H 0 0 0 0 0 0 0 0 0 0 0 0 5.8102 -1.6578 0.8710 H 0 0 0 0 0 0 0 0 0 0 0 0 5.1920 -1.2514 -0.7329 H 0 0 0 0 0 0 0 0 0 0 0 0 4.5121 -1.1666 4.1259 H 0 0 0 0 0 0 0 0 0 0 0 0 3.3670 -3.1277 0.4587 H 0 0 0 0 0 0 0 0 0 0 0 0 3.4270 -2.2383 -1.0210 H 0 0 0 0 0 0 0 0 0 0 0 0 1.2707 -2.4266 1.1484 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1958 -2.9556 -0.5826 H 0 0 0 0 0 0 0 0 0 0 0 0 2.6666 -0.4761 -1.5156 H 0 0 0 0 0 0 0 0 0 0 0 0 1.3472 -1.4226 -2.1298 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1096 0.3357 -2.0667 H 0 0 0 0 0 0 0 0 0 0 0 0 1.2586 1.0641 2.7187 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0552 1.1909 0.0489 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4795 -1.5222 1.8770 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.0255 -1.6449 0.8687 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.9048 -0.6093 2.2716 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3418 1.2326 2.3564 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3163 2.1727 1.2656 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8729 2.6280 1.4690 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.0639 2.8776 -0.0842 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.0979 1.8577 -0.4560 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.0089 0.3929 0.7376 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.1141 -0.9181 -2.0472 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.7406 -1.8229 -1.4085 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.0459 -1.1221 -0.2993 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1663 1.9496 -2.4152 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.7917 0.4207 -3.2426 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.9436 1.4406 -2.3553 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8368 1.3455 -1.1124 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8012 -1.5714 -1.9877 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7227 -0.0572 -2.8685 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8329 0.7422 -1.8865 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5517 -0.9800 -2.5407 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0817 -2.3585 -0.2943 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6123 -2.7897 0.5935 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6698 -2.6903 -1.2381 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2602 0.5673 2.0598 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 5 6 1 0 6 7 1 0 7 8 1 1 8 9 2 0 8 10 1 0 7 11 1 0 11 12 1 0 12 13 1 0 13 14 1 6 13 15 1 0 15 16 2 0 16 17 1 0 17 18 2 0 17 19 1 0 19 20 1 0 20 21 1 1 20 22 1 0 22 23 1 0 23 24 1 0 24 25 1 0 24 26 1 0 26 27 1 0 26 28 1 0 26 29 1 0 29 30 1 0 30 31 1 0 31 32 1 0 32 33 1 1 15 34 1 0 34 2 1 0 34 7 1 0 32 13 1 0 32 19 1 0 29 20 1 0 1 35 1 0 1 36 1 0 1 37 1 0 2 38 1 6 3 39 1 6 4 40 1 0 4 41 1 0 4 42 1 0 5 43 1 0 5 44 1 0 6 45 1 0 6 46 1 0 10 47 1 0 11 48 1 0 11 49 1 0 12 50 1 0 12 51 1 0 14 52 1 0 14 53 1 0 14 54 1 0 16 55 1 0 19 56 1 6 21 57 1 0 21 58 1 0 21 59 1 0 22 60 1 0 22 61 1 0 23 62 1 0 23 63 1 0 24 64 1 6 25 65 1 0 27 66 1 0 27 67 1 0 27 68 1 0 28 69 1 0 28 70 1 0 28 71 1 0 29 72 1 6 30 73 1 0 30 74 1 0 31 75 1 0 31 76 1 0 33 77 1 0 33 78 1 0 33 79 1 0 34 80 1 1 M END

Standard InCHIKey	MDQJVSLVPQYJLP-HUWCOUCRSA-N
Standard InCHI	InChI=1S/C30H46O4/c1-17-8-13-30(25(33)34)15-14-28(6)19(23(30)18(17)2)16-20(31)24-27(5)11-10-22(32)26(3,4)21(27)9-12-29(24,28)7/h16-18,21-24,32H,8-15H2,1-7H3,(H,33,34)/t17-,18+,21+,22+,23+,24-,27+,28-,29-,30+/m1/s1
SMILES	C[C@H]1[C@H](C)CC[C@]2(C(=O)O)CC[C@]3(C)C(=CC(=O)[C@@H]4[C@@]5(C)CC[C@H](O)C(C)(C)[C@@H]5CC[C@]43C)[C@H]12

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
NPO56911	Eucalyptus camaldulensis var. obtusa	Species	Myrtaceae	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
NPT1137	Individual protein	11-beta-hydroxysteroid dehydrogenase 1	Homo sapiens	IC50	=	2060.0	nM	PMID[20100662]

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 NPC610635 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	18590
0.1-0.2	26155
0.2-0.3	4127
0.3-0.4	759
0.4-0.5	165
0.5-0.6	44
0.6-0.7	11
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
0.7164	Intermediate Similarity	NPC51700
0.7164	Intermediate Similarity	NPC88716
0.7164	Intermediate Similarity	NPC68160
0.7143	Intermediate Similarity	NPC117663
0.662	Remote Similarity	NPC4036
0.662	Remote Similarity	NPC65120
0.662	Remote Similarity	NPC145067
0.662	Remote Similarity	NPC233455
0.662	Remote Similarity	NPC158030
0.6522	Remote Similarity	NPC274330
0.6418	Remote Similarity	NPC602872
0.6143	Remote Similarity	NPC479748
0.6111	Remote Similarity	NPC61543
0.6111	Remote Similarity	NPC293048
0.6111	Remote Similarity	NPC225585
0.5833	Remote Similarity	NPC272075
0.5811	Remote Similarity	NPC293564
0.5811	Remote Similarity	NPC479077
0.5753	Remote Similarity	NPC479079
0.5676	Remote Similarity	NPC71074
0.5676	Remote Similarity	NPC605937
0.56	Remote Similarity	NPC139570
0.56	Remote Similarity	NPC173089
0.557	Remote Similarity	NPC481320
0.5541	Remote Similarity	NPC290481
0.5479	Remote Similarity	NPC274050
0.5479	Remote Similarity	NPC162632
0.5479	Remote Similarity	NPC242631
0.5405	Remote Similarity	NPC480946
0.5405	Remote Similarity	NPC187722
0.5405	Remote Similarity	NPC130577
0.5405	Remote Similarity	NPC142415
0.5405	Remote Similarity	NPC102683
0.5405	Remote Similarity	NPC214756
0.5405	Remote Similarity	NPC295643
0.5395	Remote Similarity	NPC98874
0.5395	Remote Similarity	NPC202728
0.5395	Remote Similarity	NPC158059
0.5395	Remote Similarity	NPC148523
0.5333	Remote Similarity	NPC182797
0.5333	Remote Similarity	NPC52169
0.5333	Remote Similarity	NPC195019
0.5333	Remote Similarity	NPC488562
0.5256	Remote Similarity	NPC481316
0.5256	Remote Similarity	NPC607666
0.5256	Remote Similarity	NPC608261
0.5256	Remote Similarity	NPC611078
0.5222	Remote Similarity	NPC475457
0.5195	Remote Similarity	NPC40092
0.5195	Remote Similarity	NPC87095
0.5195	Remote Similarity	NPC32407
0.5195	Remote Similarity	NPC263548
0.5195	Remote Similarity	NPC606320
0.519	Remote Similarity	NPC471966
0.5185	Remote Similarity	NPC230151
0.5132	Remote Similarity	NPC606443
0.5128	Remote Similarity	NPC485589
0.5128	Remote Similarity	NPC91010
0.5063	Remote Similarity	NPC608622

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC610635 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	5803
0.1-0.2	3241
0.2-0.3	96
0.3-0.4	5
0.4-0.5	4
0.5-0.6	0
0.6-0.7	1
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
0.662	Remote 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