Structure

Physi-Chem Properties

Molecular Weight:  488.0
Volume:  371.778
LogP:  4.282
LogD:  3.762
LogS:  -4.152
# Rotatable Bonds:  3
TPSA:  55.76
# H-Bond Aceptor:  4
# H-Bond Donor:  1
# Rings:  2
# Heavy Atoms:  7

MedChem Properties

QED Drug-Likeness Score:  0.466
Synthetic Accessibility Score:  5.027
Fsp3:  0.941
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  2
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.622
MDCK Permeability:  3.4026772482320666e-05
Pgp-inhibitor:  0.999
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.031
20% Bioavailability (F20%):  0.083
30% Bioavailability (F30%):  0.949

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.932
Plasma Protein Binding (PPB):  88.2596664428711%
Volume Distribution (VD):  1.936
Pgp-substrate:  18.16834831237793%

ADMET: Metabolism

CYP1A2-inhibitor:  0.127
CYP1A2-substrate:  0.286
CYP2C19-inhibitor:  0.114
CYP2C19-substrate:  0.779
CYP2C9-inhibitor:  0.826
CYP2C9-substrate:  0.069
CYP2D6-inhibitor:  0.003
CYP2D6-substrate:  0.129
CYP3A4-inhibitor:  0.525
CYP3A4-substrate:  0.792

ADMET: Excretion

Clearance (CL):  3.711
Half-life (T1/2):  0.253

ADMET: Toxicity

hERG Blockers:  0.112
Human Hepatotoxicity (H-HT):  0.631
Drug-inuced Liver Injury (DILI):  0.809
AMES Toxicity:  0.353
Rat Oral Acute Toxicity:  0.587
Maximum Recommended Daily Dose:  0.853
Skin Sensitization:  0.636
Carcinogencity:  0.664
Eye Corrosion:  0.977
Eye Irritation:  0.573
Respiratory Toxicity:  0.983

Download Data

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

  Natural Product: NPC469556

Natural Product ID:  NPC469556
Common Name*:   (5S)-5-Hydroxyacetylcaespitol
IUPAC Name:   [(2S,3S,5S)-5-bromo-2-[(1S,2S,4R,5R)-5-bromo-4-chloro-2-hydroxy-4-methylcyclohexyl]-2,6,6-trimethyloxan-3-yl] acetate
Synonyms:   (5S)-5-Hydroxyacetylcaespitol
Standard InCHIKey:  ATUFLYZIGVYGQQ-NCIZBFQTSA-N
Standard InCHI:  InChI=1S/C17H27Br2ClO4/c1-9(21)23-14-7-12(18)15(2,3)24-17(14,5)10-6-13(19)16(4,20)8-11(10)22/h10-14,22H,6-8H2,1-5H3/t10-,11-,12-,13+,14-,16+,17-/m0/s1
SMILES:  CC(=O)O[C@H]1C[C@H](Br)C(O[C@@]1(C)[C@H]1C[C@@H](Br)[C@](C[C@@H]1O)(C)Cl)(C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1087145
PubChem CID:   46881025
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000129] Alcohols and polyols
          • [CHEMONTID:0001661] Secondary alcohols
            • [CHEMONTID:0002647] Cyclohexanols

*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
NPO29486 Laurencia catarinensis Species Rhodomelaceae Eukaryota n.a. Brazilian n.a. PMID[20039643]
NPO29486 Laurencia catarinensis Species Rhodomelaceae 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 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
NPT139 Cell Line HT-29 Homo sapiens IC50 = 70400.0 nM PMID[493312]
NPT83 Cell Line MCF7 Homo sapiens IC50 = 73600.0 nM PMID[493312]
NPT762 Cell Line A-431 Homo sapiens IC50 = 72100.0 nM PMID[493312]

☑ 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 NPC469556 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 NPC469555
0.9487 High Similarity NPC469580
0.8974 High Similarity NPC469581
0.8718 High Similarity NPC33876
0.8718 High Similarity NPC277993
0.8354 Intermediate Similarity NPC83368
0.75 Intermediate Similarity NPC150938
0.7051 Intermediate Similarity NPC308569
0.7051 Intermediate Similarity NPC469582
0.7051 Intermediate Similarity NPC469572
0.7041 Intermediate Similarity NPC475934
0.6632 Remote Similarity NPC279260
0.6591 Remote Similarity NPC475793
0.6591 Remote Similarity NPC237510
0.6562 Remote Similarity NPC471377
0.6556 Remote Similarity NPC244002
0.6526 Remote Similarity NPC93616
0.6471 Remote Similarity NPC476928
0.6458 Remote Similarity NPC246347
0.6444 Remote Similarity NPC136424
0.642 Remote Similarity NPC185116
0.6404 Remote Similarity NPC472944
0.6404 Remote Similarity NPC472945
0.6344 Remote Similarity NPC472943
0.6344 Remote Similarity NPC472951
0.6327 Remote Similarity NPC76909
0.6304 Remote Similarity NPC252483
0.6304 Remote Similarity NPC43463
0.6304 Remote Similarity NPC191345
0.6292 Remote Similarity NPC123122
0.6277 Remote Similarity NPC470156
0.6265 Remote Similarity NPC469573
0.625 Remote Similarity NPC282598
0.6237 Remote Similarity NPC83436
0.6222 Remote Similarity NPC166250
0.6211 Remote Similarity NPC470155
0.6211 Remote Similarity NPC477446
0.6211 Remote Similarity NPC477447
0.6207 Remote Similarity NPC475786
0.6196 Remote Similarity NPC476719
0.618 Remote Similarity NPC470173
0.6136 Remote Similarity NPC253123
0.6122 Remote Similarity NPC475276
0.6122 Remote Similarity NPC471410
0.6122 Remote Similarity NPC471411
0.6111 Remote Similarity NPC476422
0.6105 Remote Similarity NPC470154
0.6105 Remote Similarity NPC211049
0.6092 Remote Similarity NPC179823
0.6082 Remote Similarity NPC18953
0.6064 Remote Similarity NPC329871
0.6042 Remote Similarity NPC202688
0.6042 Remote Similarity NPC60018
0.6042 Remote Similarity NPC154043
0.6026 Remote Similarity NPC291724
0.6026 Remote Similarity NPC274261
0.6022 Remote Similarity NPC307865
0.6022 Remote Similarity NPC171658
0.6 Remote Similarity NPC186594
0.6 Remote Similarity NPC475817
0.5979 Remote Similarity NPC111582
0.5979 Remote Similarity NPC477285
0.596 Remote Similarity NPC155531
0.596 Remote Similarity NPC215968
0.5957 Remote Similarity NPC471045
0.5957 Remote Similarity NPC177343
0.5952 Remote Similarity NPC204173
0.5938 Remote Similarity NPC116320
0.5938 Remote Similarity NPC119922
0.5934 Remote Similarity NPC476718
0.5914 Remote Similarity NPC474020
0.5914 Remote Similarity NPC30575
0.5914 Remote Similarity NPC470176
0.59 Remote Similarity NPC110365
0.59 Remote Similarity NPC62202
0.59 Remote Similarity NPC45833
0.59 Remote Similarity NPC213658
0.5895 Remote Similarity NPC476603
0.5889 Remote Similarity NPC471879
0.5876 Remote Similarity NPC477286
0.5876 Remote Similarity NPC216800
0.5876 Remote Similarity NPC286719
0.587 Remote Similarity NPC74639
0.5859 Remote Similarity NPC313115
0.5859 Remote Similarity NPC476715
0.5859 Remote Similarity NPC266651
0.5851 Remote Similarity NPC474003
0.5842 Remote Similarity NPC476379
0.5842 Remote Similarity NPC471221
0.5842 Remote Similarity NPC470872
0.5833 Remote Similarity NPC474714
0.5824 Remote Similarity NPC157777
0.5824 Remote Similarity NPC131506
0.5816 Remote Similarity NPC2572
0.5816 Remote Similarity NPC67158
0.5816 Remote Similarity NPC69953
0.5816 Remote Similarity NPC30102
0.5816 Remote Similarity NPC128816
0.5816 Remote Similarity NPC29342
0.5816 Remote Similarity NPC97491
0.5816 Remote Similarity NPC273356
0.5806 Remote Similarity NPC472952
0.5806 Remote Similarity NPC472950
0.58 Remote Similarity NPC477283
0.58 Remote Similarity NPC475684
0.5789 Remote Similarity NPC272841
0.5773 Remote Similarity NPC73515
0.5773 Remote Similarity NPC190940
0.5758 Remote Similarity NPC79308
0.5745 Remote Similarity NPC470174
0.5743 Remote Similarity NPC5943
0.5743 Remote Similarity NPC280810
0.5743 Remote Similarity NPC44538
0.5729 Remote Similarity NPC31330
0.5729 Remote Similarity NPC220379
0.5729 Remote Similarity NPC476176
0.5714 Remote Similarity NPC178949
0.5714 Remote Similarity NPC2096
0.5714 Remote Similarity NPC208912
0.5714 Remote Similarity NPC247877
0.5714 Remote Similarity NPC309127
0.5714 Remote Similarity NPC191915
0.5714 Remote Similarity NPC151214
0.5714 Remote Similarity NPC47663
0.5714 Remote Similarity NPC96736
0.57 Remote Similarity NPC477205
0.57 Remote Similarity NPC235402
0.57 Remote Similarity NPC51267
0.5699 Remote Similarity NPC209666
0.5699 Remote Similarity NPC53868
0.5699 Remote Similarity NPC31046
0.5699 Remote Similarity NPC71152
0.5699 Remote Similarity NPC200167
0.5699 Remote Similarity NPC470151
0.5699 Remote Similarity NPC308489
0.5686 Remote Similarity NPC476724
0.5686 Remote Similarity NPC92370
0.5686 Remote Similarity NPC75443
0.5686 Remote Similarity NPC476435
0.5686 Remote Similarity NPC201607
0.5686 Remote Similarity NPC470260
0.5686 Remote Similarity NPC56777
0.5686 Remote Similarity NPC131453
0.5686 Remote Similarity NPC476723
0.5684 Remote Similarity NPC212453
0.5673 Remote Similarity NPC473066
0.5673 Remote Similarity NPC312805
0.567 Remote Similarity NPC15714
0.567 Remote Similarity NPC471216
0.567 Remote Similarity NPC471217
0.5667 Remote Similarity NPC301725
0.566 Remote Similarity NPC57964
0.566 Remote Similarity NPC94582
0.5657 Remote Similarity NPC259173
0.5657 Remote Similarity NPC163616
0.5657 Remote Similarity NPC213737
0.5657 Remote Similarity NPC241959
0.5657 Remote Similarity NPC474253
0.5657 Remote Similarity NPC474284
0.5657 Remote Similarity NPC474346
0.5657 Remote Similarity NPC475820
0.5652 Remote Similarity NPC157422
0.5652 Remote Similarity NPC100586
0.5652 Remote Similarity NPC109457
0.5648 Remote Similarity NPC152480
0.5647 Remote Similarity NPC470363
0.5644 Remote Similarity NPC235196
0.5644 Remote Similarity NPC131365
0.5644 Remote Similarity NPC476717
0.5644 Remote Similarity NPC64862
0.5644 Remote Similarity NPC114378
0.5644 Remote Similarity NPC228593
0.5644 Remote Similarity NPC103782
0.5638 Remote Similarity NPC186851
0.5632 Remote Similarity NPC474552
0.5632 Remote Similarity NPC235788
0.5631 Remote Similarity NPC224552
0.5631 Remote Similarity NPC291875
0.5631 Remote Similarity NPC161560
0.5631 Remote Similarity NPC239453
0.5625 Remote Similarity NPC307022
0.5619 Remote Similarity NPC256104
0.5619 Remote Similarity NPC122083
0.5619 Remote Similarity NPC211845
0.5619 Remote Similarity NPC182740
0.5619 Remote Similarity NPC475307
0.5612 Remote Similarity NPC71541
0.5612 Remote Similarity NPC216941
0.5612 Remote Similarity NPC475743
0.5612 Remote Similarity NPC118116
0.5607 Remote Similarity NPC252056
0.5607 Remote Similarity NPC237071
0.5607 Remote Similarity NPC203434
0.5607 Remote Similarity NPC156377
0.5607 Remote Similarity NPC238796
0.5604 Remote Similarity NPC470833
0.56 Remote Similarity NPC473299
0.56 Remote Similarity NPC477434
0.56 Remote Similarity NPC115995

  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 NPC469556 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
0.631 Remote Similarity NPD371 Approved
0.5816 Remote Similarity NPD3669 Approved
0.5816 Remote Similarity NPD3670 Clinical (unspecified phase)
0.5714 Remote Similarity NPD7532 Clinical (unspecified phase)
0.5699 Remote Similarity NPD1811 Approved
0.5699 Remote Similarity NPD1810 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