Structure

Physi-Chem Properties

Molecular Weight:  620.29
Volume:  582.816
LogP:  4.134
LogD:  3.044
LogS:  -3.866
# Rotatable Bonds:  8
TPSA:  117.84
# H-Bond Aceptor:  8
# H-Bond Donor:  4
# Rings:  4
# Heavy Atoms:  9

MedChem Properties

QED Drug-Likeness Score:  0.299
Synthetic Accessibility Score:  5.703
Fsp3:  1.0
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:  -4.954
MDCK Permeability:  1.0644034773577005e-05
Pgp-inhibitor:  0.993
Pgp-substrate:  0.003
Human Intestinal Absorption (HIA):  0.008
20% Bioavailability (F20%):  0.078
30% Bioavailability (F30%):  0.46

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.055
Plasma Protein Binding (PPB):  84.10969543457031%
Volume Distribution (VD):  0.691
Pgp-substrate:  9.601709365844727%

ADMET: Metabolism

CYP1A2-inhibitor:  0.003
CYP1A2-substrate:  0.687
CYP2C19-inhibitor:  0.01
CYP2C19-substrate:  0.788
CYP2C9-inhibitor:  0.075
CYP2C9-substrate:  0.02
CYP2D6-inhibitor:  0.002
CYP2D6-substrate:  0.115
CYP3A4-inhibitor:  0.232
CYP3A4-substrate:  0.575

ADMET: Excretion

Clearance (CL):  6.299
Half-life (T1/2):  0.459

ADMET: Toxicity

hERG Blockers:  0.139
Human Hepatotoxicity (H-HT):  0.748
Drug-inuced Liver Injury (DILI):  0.044
AMES Toxicity:  0.106
Rat Oral Acute Toxicity:  0.865
Maximum Recommended Daily Dose:  0.767
Skin Sensitization:  0.669
Carcinogencity:  0.268
Eye Corrosion:  0.003
Eye Irritation:  0.015
Respiratory Toxicity:  0.926

Download Data

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

  Natural Product: NPC470173

Natural Product ID:  NPC470173
Common Name*:   (5S)-2-[(2R,4As,6R,8Ar)-2-[(2S,5R)-5-Bromo-2,6,6-Trimethyloxan-2-Yl]-4A-Methyl-3,4,6,7,8,8A-Hexahydro-2H-Pyrano[3,2-B]Pyran-6-Yl]-5-[(2R,5R)-5-(2-Hydroxypropan-2-Yl)-2-Methyloxolan-2-Yl]Pentane-1,2,5-Triol
IUPAC Name:   (5S)-2-[(2R,4aS,6R,8aR)-2-[(2S,5R)-5-bromo-2,6,6-trimethyloxan-2-yl]-4a-methyl-3,4,6,7,8,8a-hexahydro-2H-pyrano[3,2-b]pyran-6-yl]-5-[(2R,5R)-5-(2-hydroxypropan-2-yl)-2-methyloxolan-2-yl]pentane-1,2,5-triol
Synonyms:  
Standard InCHIKey:  WOTQHMQYYJZPOX-HCLDQNBKSA-N
Standard InCHI:  InChI=1S/C30H53BrO8/c1-25(2,34)21-12-15-27(5,37-21)20(33)11-17-30(35,18-32)24-9-8-22-28(6,38-24)16-13-23(36-22)29(7)14-10-19(31)26(3,4)39-29/h19-24,32-35H,8-18H2,1-7H3/t19-,20+,21-,22-,23-,24-,27-,28+,29+,30?/m1/s1
SMILES:  OCC([C@H]1CC[C@@H]2[C@](O1)(C)CC[C@@H](O2)[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:   CHEMBL1806664
PubChem CID:   53377321
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 = 4600.0 nM PMID[545553]
NPT165 Cell Line HeLa Homo sapiens IC50 = 24000.0 nM PMID[545553]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. IC50 = 21000.0 nM PMID[545553]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. IC50 = 18000.0 nM PMID[545553]

☑ 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 NPC470173 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
0.9697 High Similarity NPC253123
0.9429 High Similarity NPC470176
0.9155 High Similarity NPC470174
0.9028 High Similarity NPC244002
0.8312 Intermediate Similarity NPC5361
0.7901 Intermediate Similarity NPC470175
0.7901 Intermediate Similarity NPC51267
0.7831 Intermediate Similarity NPC231784
0.7805 Intermediate Similarity NPC247826
0.7778 Intermediate Similarity NPC115995
0.7632 Intermediate Similarity NPC138273
0.7361 Intermediate Similarity NPC476702
0.7297 Intermediate Similarity NPC477759
0.7297 Intermediate Similarity NPC477754
0.7297 Intermediate Similarity NPC477760
0.7297 Intermediate Similarity NPC477761
0.7297 Intermediate Similarity NPC477758
0.7162 Intermediate Similarity NPC477752
0.7162 Intermediate Similarity NPC477751
0.7162 Intermediate Similarity NPC477756
0.7162 Intermediate Similarity NPC477764
0.7 Intermediate Similarity NPC322148
0.7 Intermediate Similarity NPC279575
0.6944 Remote Similarity NPC472026
0.6897 Remote Similarity NPC51662
0.6875 Remote Similarity NPC472952
0.6875 Remote Similarity NPC472950
0.6842 Remote Similarity NPC179823
0.675 Remote Similarity NPC166250
0.6747 Remote Similarity NPC170595
0.6712 Remote Similarity NPC477755
0.6712 Remote Similarity NPC477757
0.6712 Remote Similarity NPC477750
0.6712 Remote Similarity NPC477753
0.6712 Remote Similarity NPC477762
0.6712 Remote Similarity NPC477763
0.6707 Remote Similarity NPC474003
0.6627 Remote Similarity NPC43463
0.6627 Remote Similarity NPC272841
0.6627 Remote Similarity NPC177343
0.6625 Remote Similarity NPC470659
0.6625 Remote Similarity NPC470660
0.6625 Remote Similarity NPC83368
0.6622 Remote Similarity NPC172622
0.6585 Remote Similarity NPC136424
0.6585 Remote Similarity NPC293223
0.6582 Remote Similarity NPC471879
0.6579 Remote Similarity NPC250836
0.6548 Remote Similarity NPC81074
0.6548 Remote Similarity NPC477282
0.6543 Remote Similarity NPC470151
0.6543 Remote Similarity NPC308489
0.6538 Remote Similarity NPC67099
0.6528 Remote Similarity NPC219040
0.6528 Remote Similarity NPC472025
0.6522 Remote Similarity NPC18724
0.6522 Remote Similarity NPC470623
0.6522 Remote Similarity NPC323231
0.6522 Remote Similarity NPC171741
0.6522 Remote Similarity NPC224003
0.6517 Remote Similarity NPC314364
0.6512 Remote Similarity NPC470155
0.6512 Remote Similarity NPC477446
0.6512 Remote Similarity NPC477447
0.6506 Remote Similarity NPC133596
0.6506 Remote Similarity NPC188793
0.6506 Remote Similarity NPC474574
0.6506 Remote Similarity NPC64081
0.6506 Remote Similarity NPC11907
0.6486 Remote Similarity NPC475412
0.6471 Remote Similarity NPC472943
0.6471 Remote Similarity NPC472951
0.6463 Remote Similarity NPC150938
0.6463 Remote Similarity NPC36479
0.6452 Remote Similarity NPC267238
0.6452 Remote Similarity NPC305418
0.6452 Remote Similarity NPC77717
0.6452 Remote Similarity NPC148593
0.6452 Remote Similarity NPC253611
0.6452 Remote Similarity NPC471373
0.6438 Remote Similarity NPC34877
0.6438 Remote Similarity NPC317023
0.6438 Remote Similarity NPC290179
0.6437 Remote Similarity NPC241959
0.6429 Remote Similarity NPC252483
0.6429 Remote Similarity NPC191345
0.6413 Remote Similarity NPC210759
0.6413 Remote Similarity NPC307167
0.6413 Remote Similarity NPC229801
0.6404 Remote Similarity NPC471410
0.6404 Remote Similarity NPC107603
0.6404 Remote Similarity NPC471411
0.6395 Remote Similarity NPC470156
0.6395 Remote Similarity NPC211049
0.6395 Remote Similarity NPC470154
0.6389 Remote Similarity NPC148424
0.6383 Remote Similarity NPC471425
0.6383 Remote Similarity NPC471429
0.6383 Remote Similarity NPC189575
0.6383 Remote Similarity NPC471424
0.6383 Remote Similarity NPC106701
0.6383 Remote Similarity NPC205129
0.6383 Remote Similarity NPC474399
0.6375 Remote Similarity NPC53760
0.6375 Remote Similarity NPC52268
0.6374 Remote Similarity NPC131466
0.6374 Remote Similarity NPC82955
0.6364 Remote Similarity NPC471761
0.6364 Remote Similarity NPC190418
0.6364 Remote Similarity NPC471760
0.6351 Remote Similarity NPC185116
0.6344 Remote Similarity NPC477547
0.6344 Remote Similarity NPC250393
0.6344 Remote Similarity NPC249204
0.6344 Remote Similarity NPC297348
0.6344 Remote Similarity NPC141769
0.6344 Remote Similarity NPC325828
0.6344 Remote Similarity NPC48339
0.6344 Remote Similarity NPC234352
0.6344 Remote Similarity NPC177834
0.6344 Remote Similarity NPC477451
0.6333 Remote Similarity NPC140446
0.6333 Remote Similarity NPC43912
0.6329 Remote Similarity NPC473294
0.6329 Remote Similarity NPC471472
0.6322 Remote Similarity NPC475388
0.6316 Remote Similarity NPC304011
0.6316 Remote Similarity NPC139271
0.631 Remote Similarity NPC476719
0.6296 Remote Similarity NPC131506
0.6296 Remote Similarity NPC157777
0.6292 Remote Similarity NPC290612
0.6292 Remote Similarity NPC469555
0.6279 Remote Similarity NPC186594
0.6279 Remote Similarity NPC16449
0.6277 Remote Similarity NPC174024
0.6277 Remote Similarity NPC222731
0.6277 Remote Similarity NPC253268
0.6277 Remote Similarity NPC312678
0.6277 Remote Similarity NPC471464
0.6277 Remote Similarity NPC291203
0.6277 Remote Similarity NPC264101
0.6277 Remote Similarity NPC131693
0.6277 Remote Similarity NPC473851
0.6277 Remote Similarity NPC45959
0.6277 Remote Similarity NPC475436
0.6277 Remote Similarity NPC217205
0.6277 Remote Similarity NPC291547
0.6277 Remote Similarity NPC252253
0.6277 Remote Similarity NPC294686
0.6277 Remote Similarity NPC179859
0.6265 Remote Similarity NPC231680
0.6265 Remote Similarity NPC91387
0.6265 Remote Similarity NPC270306
0.625 Remote Similarity NPC274200
0.625 Remote Similarity NPC16964
0.625 Remote Similarity NPC470833
0.6234 Remote Similarity NPC199937
0.6222 Remote Similarity NPC470657
0.6222 Remote Similarity NPC215968
0.6222 Remote Similarity NPC477283
0.6222 Remote Similarity NPC268633
0.6222 Remote Similarity NPC155531
0.622 Remote Similarity NPC39266
0.622 Remote Similarity NPC476709
0.622 Remote Similarity NPC206823
0.622 Remote Similarity NPC169085
0.622 Remote Similarity NPC123122
0.622 Remote Similarity NPC163812
0.622 Remote Similarity NPC9763
0.622 Remote Similarity NPC248427
0.622 Remote Similarity NPC225748
0.6211 Remote Similarity NPC19400
0.6211 Remote Similarity NPC473727
0.6211 Remote Similarity NPC473610
0.6211 Remote Similarity NPC6295
0.6211 Remote Similarity NPC107962
0.6211 Remote Similarity NPC477494
0.6211 Remote Similarity NPC475351
0.6211 Remote Similarity NPC206003
0.6211 Remote Similarity NPC211354
0.6211 Remote Similarity NPC107188
0.6207 Remote Similarity NPC216941
0.6207 Remote Similarity NPC116320
0.6207 Remote Similarity NPC118116
0.6207 Remote Similarity NPC119922
0.6203 Remote Similarity NPC469925
0.619 Remote Similarity NPC329626
0.619 Remote Similarity NPC107963
0.6186 Remote Similarity NPC471374
0.6186 Remote Similarity NPC471375
0.6186 Remote Similarity NPC209798
0.6184 Remote Similarity NPC475807
0.618 Remote Similarity NPC166279
0.618 Remote Similarity NPC320824
0.618 Remote Similarity NPC18953
0.618 Remote Similarity NPC474156
0.618 Remote Similarity NPC469556
0.617 Remote Similarity NPC144790
0.617 Remote Similarity NPC137004

  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 NPC470173 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
0.6667 Remote Similarity NPD371 Approved
0.6375 Remote Similarity NPD7532 Clinical (unspecified phase)
0.6344 Remote Similarity NPD8171 Discontinued
0.6267 Remote Similarity NPD6123 Approved
0.6145 Remote Similarity NPD1811 Approved
0.6145 Remote Similarity NPD1810 Approved
0.5972 Remote Similarity NPD888 Phase 3
0.5972 Remote Similarity NPD893 Approved
0.5972 Remote Similarity NPD894 Approved
0.5972 Remote Similarity NPD890 Clinical (unspecified phase)
0.5972 Remote Similarity NPD887 Approved
0.5972 Remote Similarity NPD891 Phase 3
0.5972 Remote Similarity NPD892 Phase 3
0.5972 Remote Similarity NPD895 Approved
0.5972 Remote Similarity NPD889 Approved
0.5946 Remote Similarity NPD2267 Suspended
0.589 Remote Similarity NPD7346 Approved
0.5854 Remote Similarity NPD4267 Clinical (unspecified phase)
0.5833 Remote Similarity NPD2269 Approved
0.5783 Remote Similarity NPD2687 Approved
0.5783 Remote Similarity NPD2686 Approved
0.5783 Remote Similarity NPD2254 Approved
0.573 Remote Similarity NPD6928 Phase 2
0.5728 Remote Similarity NPD8170 Clinical (unspecified phase)
0.5714 Remote Similarity NPD3670 Clinical (unspecified phase)
0.5714 Remote Similarity NPD3669 Approved
0.5694 Remote Similarity NPD904 Phase 3
0.5694 Remote Similarity NPD905 Approved
0.5606 Remote Similarity NPD7536 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