Structure

Physi-Chem Properties

Molecular Weight:  636.29
Volume:  597.526
LogP:  3.515
LogD:  2.436
LogS:  -3.451
# Rotatable Bonds:  11
TPSA:  145.91
# H-Bond Aceptor:  9
# H-Bond Donor:  5
# Rings:  3
# Heavy Atoms:  10

MedChem Properties

QED Drug-Likeness Score:  0.216
Synthetic Accessibility Score:  5.601
Fsp3:  0.967
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  1
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.975
MDCK Permeability:  7.681255738134496e-06
Pgp-inhibitor:  0.984
Pgp-substrate:  0.026
Human Intestinal Absorption (HIA):  0.013
20% Bioavailability (F20%):  0.814
30% Bioavailability (F30%):  0.487

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.328
Plasma Protein Binding (PPB):  77.6668472290039%
Volume Distribution (VD):  0.658
Pgp-substrate:  11.220646858215332%

ADMET: Metabolism

CYP1A2-inhibitor:  0.002
CYP1A2-substrate:  0.664
CYP2C19-inhibitor:  0.012
CYP2C19-substrate:  0.737
CYP2C9-inhibitor:  0.053
CYP2C9-substrate:  0.033
CYP2D6-inhibitor:  0.002
CYP2D6-substrate:  0.077
CYP3A4-inhibitor:  0.141
CYP3A4-substrate:  0.63

ADMET: Excretion

Clearance (CL):  4.744
Half-life (T1/2):  0.76

ADMET: Toxicity

hERG Blockers:  0.039
Human Hepatotoxicity (H-HT):  0.595
Drug-inuced Liver Injury (DILI):  0.1
AMES Toxicity:  0.526
Rat Oral Acute Toxicity:  0.885
Maximum Recommended Daily Dose:  0.879
Skin Sensitization:  0.391
Carcinogencity:  0.795
Eye Corrosion:  0.003
Eye Irritation:  0.012
Respiratory Toxicity:  0.083

Download Data

Data Type Select
General Info & Identifiers & Properties  
Structure MOL file  
Source Organisms  
Biological Activities  
Similar NPs/Drugs  

  Natural Product: NPC115995

Natural Product ID:  NPC115995
Common Name*:   Prethyrsenol A
IUPAC Name:   (4R,7S)-1-[(2R,3S,6R)-6-[(2S,5R)-5-bromo-2,6,6-trimethyloxan-2-yl]-3-hydroxy-3-methyloxan-2-yl]-4,7-dihydroxy-4-(hydroxymethyl)-7-[(2R,5R)-5-(2-hydroxypropan-2-yl)-2-methyloxolan-2-yl]heptan-3-one
Synonyms:   Prethyrsenol A
Standard InCHIKey:  XJSFNGPNIJKOBD-ROPSBFFGSA-N
Standard InCHI:  InChI=1S/C30H53BrO9/c1-25(2,35)22-13-16-28(6,39-22)20(33)11-17-30(37,18-32)21(34)8-9-23-27(5,36)14-12-24(38-23)29(7)15-10-19(31)26(3,4)40-29/h19-20,22-24,32-33,35-37H,8-18H2,1-7H3/t19-,20+,22-,23-,24-,27+,28-,29+,30-/m1/s1
SMILES:  OC[C@@](C(=O)CC[C@H]1O[C@H](CC[C@]1(C)O)[C@]1(C)CC[C@H](C(O1)(C)C)Br)(CC[C@@H]([C@@]1(C)CC[C@@H](O1)C(O)(C)C)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1806662
PubChem CID:   53377320
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001553] Triterpenoids

*Note: the InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
**Note: the Chemical Classification was calculated by NPClassifier Version 1.5. Reference: PMID:34662515.

  Species Source

Organism ID Organism Name Taxonomy Level Family SuperKingdom Isolation Part Collection Location Collection Time Reference
NPO3322 Laurencia viridis Species Rhodomelaceae Eukaryota n.a. n.a. n.a. PMID[21616566]

☑ 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 NP ID 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

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT15 Cell Line Jurkat Homo sapiens IC50 = 8150.0 nM PMID[525536]
NPT165 Cell Line HeLa Homo sapiens IC50 = 29000.0 nM PMID[525536]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. IC50 = 10200.0 nM PMID[525536]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. IC50 = 14500.0 nM PMID[525536]

☑ Note for Activity Records:
☉ The quantitative biological activities were primarily integrated from ChEMBL (Version-30) database and were also directly collected from PubMed literature. PubMed PMID was provided as the reference link for each activity record.

  Chemically structural similarity: I. Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes 4,3285 NPs with experimentally-derived bioactivity available in NPASS)

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules. Tc lies between [0, 1] where '1' indicates the highest similarity. What is Tanimoto coefficient

●  The left chart: Distribution of similarity level between NPC115995 and all remaining natural products in the NPASS database.
●  The right table: Most similar natural products (Tc>=0.56 or Top200).

Similarity Score Similarity Level Natural Product ID
0.9873 High Similarity NPC51267
0.7952 Intermediate Similarity NPC474003
0.7778 Intermediate Similarity NPC470173
0.775 Intermediate Similarity NPC253123
0.7738 Intermediate Similarity NPC244002
0.7473 Intermediate Similarity NPC314364
0.7412 Intermediate Similarity NPC470176
0.7209 Intermediate Similarity NPC470174
0.7113 Intermediate Similarity NPC322188
0.7097 Intermediate Similarity NPC51662
0.7073 Intermediate Similarity NPC469925
0.7053 Intermediate Similarity NPC65359
0.7045 Intermediate Similarity NPC475616
0.6989 Remote Similarity NPC476717
0.6947 Remote Similarity NPC477440
0.6947 Remote Similarity NPC477443
0.6875 Remote Similarity NPC477444
0.6875 Remote Similarity NPC477442
0.6875 Remote Similarity NPC477433
0.6869 Remote Similarity NPC39859
0.6869 Remote Similarity NPC76862
0.6869 Remote Similarity NPC470883
0.6869 Remote Similarity NPC158416
0.6867 Remote Similarity NPC286842
0.686 Remote Similarity NPC473775
0.686 Remote Similarity NPC51249
0.686 Remote Similarity NPC473699
0.686 Remote Similarity NPC475260
0.686 Remote Similarity NPC475232
0.686 Remote Similarity NPC474100
0.6813 Remote Similarity NPC5361
0.6809 Remote Similarity NPC470657
0.6804 Remote Similarity NPC469627
0.679 Remote Similarity NPC235788
0.6737 Remote Similarity NPC31349
0.6733 Remote Similarity NPC274695
0.6705 Remote Similarity NPC228411
0.67 Remote Similarity NPC476009
0.6667 Remote Similarity NPC469870
0.6667 Remote Similarity NPC247877
0.6667 Remote Similarity NPC309127
0.6667 Remote Similarity NPC469871
0.6667 Remote Similarity NPC292458
0.6667 Remote Similarity NPC470014
0.6667 Remote Similarity NPC217559
0.6667 Remote Similarity NPC478038
0.6667 Remote Similarity NPC268578
0.6633 Remote Similarity NPC329952
0.6633 Remote Similarity NPC216137
0.6632 Remote Similarity NPC475729
0.6632 Remote Similarity NPC474215
0.6627 Remote Similarity NPC469926
0.6604 Remote Similarity NPC469788
0.6604 Remote Similarity NPC290247
0.6604 Remote Similarity NPC176756
0.6604 Remote Similarity NPC469787
0.66 Remote Similarity NPC17336
0.66 Remote Similarity NPC475900
0.66 Remote Similarity NPC470191
0.6596 Remote Similarity NPC473791
0.6596 Remote Similarity NPC475963
0.6596 Remote Similarity NPC151176
0.6596 Remote Similarity NPC477434
0.6596 Remote Similarity NPC3464
0.6596 Remote Similarity NPC475689
0.6591 Remote Similarity NPC125164
0.6588 Remote Similarity NPC82315
0.6569 Remote Similarity NPC253995
0.6566 Remote Similarity NPC61275
0.6556 Remote Similarity NPC214030
0.6556 Remote Similarity NPC83108
0.6552 Remote Similarity NPC96322
0.6542 Remote Similarity NPC167044
0.6538 Remote Similarity NPC470172
0.6538 Remote Similarity NPC227622
0.6538 Remote Similarity NPC471254
0.6538 Remote Similarity NPC80640
0.6535 Remote Similarity NPC477264
0.6526 Remote Similarity NPC470175
0.6526 Remote Similarity NPC477445
0.6526 Remote Similarity NPC476715
0.6522 Remote Similarity NPC472948
0.6514 Remote Similarity NPC473062
0.6512 Remote Similarity NPC28526
0.65 Remote Similarity NPC329713
0.65 Remote Similarity NPC76136
0.65 Remote Similarity NPC190294
0.65 Remote Similarity NPC217567
0.6495 Remote Similarity NPC477614
0.6495 Remote Similarity NPC231784
0.6495 Remote Similarity NPC226491
0.6495 Remote Similarity NPC471221
0.6484 Remote Similarity NPC478084
0.6481 Remote Similarity NPC217041
0.6481 Remote Similarity NPC87393
0.6476 Remote Similarity NPC473406
0.6476 Remote Similarity NPC471253
0.6471 Remote Similarity NPC323421
0.6471 Remote Similarity NPC74466
0.6471 Remote Similarity NPC328562
0.6465 Remote Similarity NPC474699
0.6465 Remote Similarity NPC146852
0.6463 Remote Similarity NPC469923
0.6463 Remote Similarity NPC10659
0.6458 Remote Similarity NPC477441
0.6458 Remote Similarity NPC247826
0.6458 Remote Similarity NPC80700
0.6449 Remote Similarity NPC137453
0.6442 Remote Similarity NPC298266
0.6442 Remote Similarity NPC259654
0.6442 Remote Similarity NPC178853
0.6442 Remote Similarity NPC162024
0.6436 Remote Similarity NPC287354
0.6436 Remote Similarity NPC62407
0.6429 Remote Similarity NPC173926
0.6429 Remote Similarity NPC92974
0.6429 Remote Similarity NPC474951
0.6429 Remote Similarity NPC200580
0.6429 Remote Similarity NPC67653
0.6429 Remote Similarity NPC471459
0.6429 Remote Similarity NPC61688
0.6422 Remote Similarity NPC470622
0.6422 Remote Similarity NPC182185
0.6422 Remote Similarity NPC66513
0.6415 Remote Similarity NPC267637
0.6415 Remote Similarity NPC470167
0.6408 Remote Similarity NPC83895
0.6408 Remote Similarity NPC255592
0.6408 Remote Similarity NPC308567
0.6408 Remote Similarity NPC187761
0.6408 Remote Similarity NPC261377
0.6404 Remote Similarity NPC138273
0.6404 Remote Similarity NPC215030
0.64 Remote Similarity NPC478037
0.64 Remote Similarity NPC474379
0.64 Remote Similarity NPC478036
0.6392 Remote Similarity NPC179659
0.6392 Remote Similarity NPC470920
0.6381 Remote Similarity NPC313569
0.6373 Remote Similarity NPC31645
0.6373 Remote Similarity NPC476728
0.6364 Remote Similarity NPC185419
0.6364 Remote Similarity NPC184550
0.6364 Remote Similarity NPC157476
0.6355 Remote Similarity NPC41674
0.6355 Remote Similarity NPC168890
0.6355 Remote Similarity NPC184805
0.6355 Remote Similarity NPC228311
0.6355 Remote Similarity NPC469441
0.6355 Remote Similarity NPC273189
0.6354 Remote Similarity NPC477205
0.6346 Remote Similarity NPC80417
0.6337 Remote Similarity NPC470424
0.6337 Remote Similarity NPC470423
0.6337 Remote Similarity NPC206878
0.633 Remote Similarity NPC313668
0.633 Remote Similarity NPC315836
0.6327 Remote Similarity NPC476708
0.6327 Remote Similarity NPC177629
0.6327 Remote Similarity NPC90676
0.6327 Remote Similarity NPC476706
0.6327 Remote Similarity NPC476707
0.6327 Remote Similarity NPC470009
0.6327 Remote Similarity NPC476435
0.6327 Remote Similarity NPC58219
0.6322 Remote Similarity NPC285003
0.6322 Remote Similarity NPC241265
0.6316 Remote Similarity NPC227170
0.6316 Remote Similarity NPC476721
0.6311 Remote Similarity NPC278028
0.6311 Remote Similarity NPC470632
0.6311 Remote Similarity NPC328180
0.6311 Remote Similarity NPC266842
0.6311 Remote Similarity NPC40812
0.6306 Remote Similarity NPC98870
0.6304 Remote Similarity NPC475725
0.63 Remote Similarity NPC111883
0.6296 Remote Similarity NPC203974
0.6296 Remote Similarity NPC471430
0.6292 Remote Similarity NPC308096
0.6292 Remote Similarity NPC291228
0.6289 Remote Similarity NPC472745
0.6289 Remote Similarity NPC474762
0.6289 Remote Similarity NPC476015
0.6289 Remote Similarity NPC469626
0.6289 Remote Similarity NPC476726
0.6289 Remote Similarity NPC92139
0.6289 Remote Similarity NPC475019
0.6289 Remote Similarity NPC474949
0.6289 Remote Similarity NPC476727
0.6289 Remote Similarity NPC475276
0.6289 Remote Similarity NPC475491
0.6286 Remote Similarity NPC47880
0.6286 Remote Similarity NPC181645
0.6283 Remote Similarity NPC173686
0.6283 Remote Similarity NPC213084
0.6283 Remote Similarity NPC190185
0.6283 Remote Similarity NPC16081
0.6277 Remote Similarity NPC475270
0.6277 Remote Similarity NPC475667

  Chemically structural similarity: II. Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC115995 and all drugs/candidates.
●  The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

Similarity Score Similarity Level Drug ID Developmental Stage
0.6538 Remote Similarity NPD8085 Approved
0.6538 Remote Similarity NPD8139 Approved
0.6538 Remote Similarity NPD8086 Approved
0.6538 Remote Similarity NPD8084 Approved
0.6538 Remote Similarity NPD8082 Approved
0.6538 Remote Similarity NPD8083 Approved
0.6538 Remote Similarity NPD8138 Approved
0.6477 Remote Similarity NPD3181 Approved
0.6476 Remote Similarity NPD8275 Approved
0.6476 Remote Similarity NPD8276 Approved
0.6415 Remote Similarity NPD8081 Approved
0.6355 Remote Similarity NPD8393 Approved
0.6239 Remote Similarity NPD5345 Clinical (unspecified phase)
0.6237 Remote Similarity NPD7329 Approved
0.6129 Remote Similarity NPD4238 Approved
0.6129 Remote Similarity NPD4802 Phase 2
0.6118 Remote Similarity NPD7909 Approved
0.6111 Remote Similarity NPD4057 Clinical (unspecified phase)
0.6111 Remote Similarity NPD4056 Clinical (unspecified phase)
0.6111 Remote Similarity NPD8170 Clinical (unspecified phase)
0.6092 Remote Similarity NPD896 Approved
0.6092 Remote Similarity NPD898 Approved
0.6092 Remote Similarity NPD897 Approved
0.6019 Remote Similarity NPD5282 Discontinued
0.6 Remote Similarity NPD8140 Approved
0.6 Remote Similarity NPD8307 Discontinued
0.5976 Remote Similarity NPD8959 Approved
0.5929 Remote Similarity NPD8413 Clinical (unspecified phase)
0.5926 Remote Similarity NPD8300 Approved
0.5926 Remote Similarity NPD8301 Approved
0.5893 Remote Similarity NPD8306 Approved
0.5893 Remote Similarity NPD8305 Approved
0.5882 Remote Similarity NPD8274 Clinical (unspecified phase)
0.5854 Remote Similarity NPD73 Approved
0.5841 Remote Similarity NPD8087 Discontinued
0.5833 Remote Similarity NPD8080 Discontinued
0.5833 Remote Similarity NPD1700 Approved
0.5825 Remote Similarity NPD7983 Approved
0.5812 Remote Similarity NPD8295 Clinical (unspecified phase)
0.5789 Remote Similarity NPD3671 Phase 1
0.575 Remote Similarity NPD6921 Approved
0.5714 Remote Similarity NPD7899 Clinical (unspecified phase)
0.5678 Remote Similarity NPD8137 Clinical (unspecified phase)
0.5657 Remote Similarity NPD3670 Clinical (unspecified phase)
0.5657 Remote Similarity NPD3669 Approved
0.5656 Remote Similarity NPD8328 Phase 3
0.5638 Remote Similarity NPD3703 Phase 2
0.5632 Remote Similarity NPD8961 Approved
0.562 Remote Similarity NPD8266 Approved
0.562 Remote Similarity NPD8268 Approved
0.562 Remote Similarity NPD8516 Approved
0.562 Remote Similarity NPD8267 Approved
0.562 Remote Similarity NPD8515 Approved
0.562 Remote Similarity NPD8517 Approved
0.562 Remote Similarity NPD8269 Approved
0.562 Remote Similarity NPD8513 Phase 3
0.5612 Remote Similarity NPD1780 Approved
0.5612 Remote Similarity NPD1779 Approved
0.561 Remote Similarity NPD3728 Approved
0.561 Remote Similarity NPD3730 Approved

  Bioactivity similarity: Similar Natural Products in NPASS

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