Structure

Physi-Chem Properties

Molecular Weight:  344.09
Volume:  337.642
LogP:  3.513
LogD:  3.271
LogS:  -4.19
# Rotatable Bonds:  8
TPSA:  35.53
# H-Bond Aceptor:  3
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.304
Synthetic Accessibility Score:  5.293
Fsp3:  0.588
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Accepted
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.393
MDCK Permeability:  1.8593269487610087e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.068
20% Bioavailability (F20%):  0.006
30% Bioavailability (F30%):  0.99

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.152
Plasma Protein Binding (PPB):  90.27519989013672%
Volume Distribution (VD):  2.16
Pgp-substrate:  3.478269577026367%

ADMET: Metabolism

CYP1A2-inhibitor:  0.147
CYP1A2-substrate:  0.179
CYP2C19-inhibitor:  0.425
CYP2C19-substrate:  0.784
CYP2C9-inhibitor:  0.317
CYP2C9-substrate:  0.064
CYP2D6-inhibitor:  0.064
CYP2D6-substrate:  0.195
CYP3A4-inhibitor:  0.898
CYP3A4-substrate:  0.362

ADMET: Excretion

Clearance (CL):  6.673
Half-life (T1/2):  0.861

ADMET: Toxicity

hERG Blockers:  0.022
Human Hepatotoxicity (H-HT):  0.431
Drug-inuced Liver Injury (DILI):  0.918
AMES Toxicity:  0.746
Rat Oral Acute Toxicity:  0.439
Maximum Recommended Daily Dose:  0.844
Skin Sensitization:  0.655
Carcinogencity:  0.547
Eye Corrosion:  0.085
Eye Irritation:  0.273
Respiratory Toxicity:  0.956

Download Data

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

  Natural Product: NPC477421

Natural Product ID:  NPC477421
Common Name*:   [(2R,3S,5S)-5-[(Z)-1-chlorohex-3-en-5-ynyl]-2-[(Z)-3-chloropent-1-enyl]oxolan-3-yl] acetate
IUPAC Name:   [(2R,3S,5S)-5-[(Z)-1-chlorohex-3-en-5-ynyl]-2-[(Z)-3-chloropent-1-enyl]oxolan-3-yl] acetate
Synonyms:  
Standard InCHIKey:  VFEVOEOMQSLWCB-FALBAKGPSA-N
Standard InCHI:  InChI=1S/C17H22Cl2O3/c1-4-6-7-8-14(19)16-11-17(21-12(3)20)15(22-16)10-9-13(18)5-2/h1,6-7,9-10,13-17H,5,8,11H2,2-3H3/b7-6-,10-9-/t13?,14?,15-,16+,17+/m1/s1
SMILES:  CCC(/C=C\[C@@H]1[C@H](C[C@H](O1)C(C/C=C\C#C)Cl)OC(=O)C)Cl
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   25227558
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates
          • [CHEMONTID:0002105] Glycosyl compounds
            • [CHEMONTID:0002204] C-glycosyl compounds

*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
NPO26797 Laurencia glandulifera Species Rhodomelaceae Eukaryota n.a. the island of Crete in the south Aegean Sea n.a. PMID[19138151]
NPO26797 Laurencia glandulifera 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 >= 10000 nM PMID[19138151]
NPT83 Cell Line MCF7 Homo sapiens IC50 >= 10000 nM PMID[19138151]
NPT306 Cell Line PC-3 Homo sapiens IC50 >= 10000 nM PMID[19138151]
NPT165 Cell Line HeLa Homo sapiens IC50 >= 10000 nM PMID[19138151]
NPT762 Cell Line A-431 Homo sapiens IC50 >= 10000 nM PMID[19138151]

☑ 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 NPC477421 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
0.8267 Intermediate Similarity NPC477422
0.7867 Intermediate Similarity NPC323677
0.7867 Intermediate Similarity NPC477423
0.7867 Intermediate Similarity NPC477429
0.7606 Intermediate Similarity NPC477424
0.7531 Intermediate Similarity NPC473947
0.7529 Intermediate Similarity NPC477428
0.7465 Intermediate Similarity NPC474267
0.7368 Intermediate Similarity NPC477431
0.725 Intermediate Similarity NPC52781
0.7183 Intermediate Similarity NPC26310
0.7143 Intermediate Similarity NPC475760
0.7093 Intermediate Similarity NPC30915
0.6944 Remote Similarity NPC471279
0.6944 Remote Similarity NPC471277
0.6892 Remote Similarity NPC299730
0.6875 Remote Similarity NPC475762
0.6875 Remote Similarity NPC473306
0.68 Remote Similarity NPC66460
0.68 Remote Similarity NPC271282
0.68 Remote Similarity NPC325929
0.6757 Remote Similarity NPC22897
0.6757 Remote Similarity NPC159650
0.6711 Remote Similarity NPC29697
0.6706 Remote Similarity NPC477088
0.6667 Remote Similarity NPC26223
0.6667 Remote Similarity NPC471278
0.6667 Remote Similarity NPC186531
0.6625 Remote Similarity NPC316572
0.6623 Remote Similarity NPC308457
0.6623 Remote Similarity NPC25747
0.6623 Remote Similarity NPC148233
0.6582 Remote Similarity NPC225272
0.6552 Remote Similarity NPC150502
0.6533 Remote Similarity NPC222852
0.6528 Remote Similarity NPC269615
0.6522 Remote Similarity NPC207815
0.6517 Remote Similarity NPC475732
0.6506 Remote Similarity NPC77724
0.6506 Remote Similarity NPC474280
0.65 Remote Similarity NPC218477
0.6494 Remote Similarity NPC54925
0.6486 Remote Similarity NPC212730
0.6486 Remote Similarity NPC265551
0.6479 Remote Similarity NPC106531
0.6477 Remote Similarity NPC474252
0.6471 Remote Similarity NPC474278
0.6471 Remote Similarity NPC474026
0.6456 Remote Similarity NPC124586
0.6456 Remote Similarity NPC284447
0.6438 Remote Similarity NPC474913
0.642 Remote Similarity NPC475004
0.6395 Remote Similarity NPC248775
0.6386 Remote Similarity NPC329914
0.6386 Remote Similarity NPC185186
0.6386 Remote Similarity NPC327383
0.6386 Remote Similarity NPC329890
0.6375 Remote Similarity NPC472266
0.6364 Remote Similarity NPC475984
0.6353 Remote Similarity NPC301525
0.6341 Remote Similarity NPC325098
0.6329 Remote Similarity NPC182794
0.6322 Remote Similarity NPC471537
0.6322 Remote Similarity NPC470148
0.6322 Remote Similarity NPC470149
0.6322 Remote Similarity NPC475210
0.6322 Remote Similarity NPC1180
0.6322 Remote Similarity NPC180725
0.6316 Remote Similarity NPC478095
0.6296 Remote Similarity NPC474823
0.6292 Remote Similarity NPC475690
0.6282 Remote Similarity NPC470965
0.6282 Remote Similarity NPC179087
0.6282 Remote Similarity NPC210303
0.6282 Remote Similarity NPC44343
0.6267 Remote Similarity NPC44542
0.6265 Remote Similarity NPC163003
0.625 Remote Similarity NPC121374
0.625 Remote Similarity NPC133226
0.625 Remote Similarity NPC470147
0.625 Remote Similarity NPC276299
0.625 Remote Similarity NPC248125
0.6235 Remote Similarity NPC327041
0.6235 Remote Similarity NPC285840
0.622 Remote Similarity NPC101622
0.6216 Remote Similarity NPC52264
0.6207 Remote Similarity NPC473471
0.6203 Remote Similarity NPC470320
0.6203 Remote Similarity NPC477457
0.6203 Remote Similarity NPC477456
0.6196 Remote Similarity NPC184461
0.619 Remote Similarity NPC470435
0.619 Remote Similarity NPC474705
0.6184 Remote Similarity NPC478096
0.6184 Remote Similarity NPC469373
0.6184 Remote Similarity NPC23418
0.6173 Remote Similarity NPC25298
0.6173 Remote Similarity NPC330426
0.6173 Remote Similarity NPC478100
0.6173 Remote Similarity NPC22101
0.6173 Remote Similarity NPC473829
0.6173 Remote Similarity NPC194871
0.6173 Remote Similarity NPC127091
0.6173 Remote Similarity NPC104537
0.6173 Remote Similarity NPC148192
0.6173 Remote Similarity NPC271921
0.6173 Remote Similarity NPC475443
0.6163 Remote Similarity NPC127118
0.6163 Remote Similarity NPC49392
0.6163 Remote Similarity NPC209113
0.6163 Remote Similarity NPC301207
0.6163 Remote Similarity NPC190400
0.6163 Remote Similarity NPC188860
0.6154 Remote Similarity NPC328776
0.6154 Remote Similarity NPC41856
0.6154 Remote Similarity NPC320305
0.6145 Remote Similarity NPC469660
0.6145 Remote Similarity NPC476037
0.6145 Remote Similarity NPC129630
0.6145 Remote Similarity NPC4299
0.6145 Remote Similarity NPC476012
0.6136 Remote Similarity NPC473981
0.6136 Remote Similarity NPC473980
0.6129 Remote Similarity NPC475405
0.6125 Remote Similarity NPC96414
0.6125 Remote Similarity NPC19769
0.6118 Remote Similarity NPC476355
0.6118 Remote Similarity NPC140287
0.6104 Remote Similarity NPC286189
0.6098 Remote Similarity NPC276290
0.6098 Remote Similarity NPC473559
0.6098 Remote Similarity NPC324981
0.6098 Remote Similarity NPC141481
0.6098 Remote Similarity NPC48218
0.6098 Remote Similarity NPC470256
0.6092 Remote Similarity NPC476028
0.6092 Remote Similarity NPC51809
0.6092 Remote Similarity NPC49302
0.6092 Remote Similarity NPC176329
0.6092 Remote Similarity NPC171204
0.6092 Remote Similarity NPC475711
0.6092 Remote Similarity NPC474818
0.6092 Remote Similarity NPC125365
0.6092 Remote Similarity NPC233071
0.6092 Remote Similarity NPC97516
0.6092 Remote Similarity NPC141789
0.6081 Remote Similarity NPC137538
0.6076 Remote Similarity NPC217940
0.6071 Remote Similarity NPC477084
0.6071 Remote Similarity NPC84038
0.6067 Remote Similarity NPC233332
0.6067 Remote Similarity NPC474739
0.6064 Remote Similarity NPC475712
0.6049 Remote Similarity NPC201356
0.6049 Remote Similarity NPC478101
0.6049 Remote Similarity NPC146811
0.6047 Remote Similarity NPC469414
0.6047 Remote Similarity NPC329826
0.6044 Remote Similarity NPC170286
0.6044 Remote Similarity NPC475947
0.6044 Remote Similarity NPC253801
0.6026 Remote Similarity NPC158368
0.6026 Remote Similarity NPC226872
0.6026 Remote Similarity NPC154908
0.6026 Remote Similarity NPC252851
0.6024 Remote Similarity NPC470436
0.6024 Remote Similarity NPC329656
0.6024 Remote Similarity NPC130618
0.6024 Remote Similarity NPC269841
0.6024 Remote Similarity NPC473772
0.6023 Remote Similarity NPC474005
0.6023 Remote Similarity NPC28049
0.6023 Remote Similarity NPC267231
0.6023 Remote Similarity NPC475699
0.6023 Remote Similarity NPC279214
0.6023 Remote Similarity NPC221095
0.6022 Remote Similarity NPC279267
0.6022 Remote Similarity NPC69082
0.6 Remote Similarity NPC10316
0.6 Remote Similarity NPC295633
0.6 Remote Similarity NPC281949
0.6 Remote Similarity NPC146551
0.6 Remote Similarity NPC328089
0.6 Remote Similarity NPC200845
0.6 Remote Similarity NPC222244
0.6 Remote Similarity NPC470963
0.6 Remote Similarity NPC128061
0.6 Remote Similarity NPC68343
0.6 Remote Similarity NPC25684
0.6 Remote Similarity NPC16349
0.6 Remote Similarity NPC28779
0.6 Remote Similarity NPC477085
0.6 Remote Similarity NPC58956
0.6 Remote Similarity NPC226592
0.6 Remote Similarity NPC474513
0.6 Remote Similarity NPC141810
0.6 Remote Similarity NPC301477
0.6 Remote Similarity NPC474894
0.6 Remote Similarity NPC133450
0.6 Remote Similarity NPC269206

  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 NPC477421 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
0.6458 Remote Similarity NPD4792 Clinical (unspecified phase)
0.6125 Remote Similarity NPD2685 Clinical (unspecified phase)
0.5745 Remote Similarity NPD1733 Clinical (unspecified phase)
0.5714 Remote Similarity NPD5790 Clinical (unspecified phase)
0.5676 Remote Similarity NPD6927 Phase 3
0.5625 Remote Similarity NPD4246 Clinical (unspecified phase)
0.5612 Remote Similarity NPD7838 Discovery
0.561 Remote Similarity NPD3197 Phase 1

  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