Structure

Physi-Chem Properties

Molecular Weight:  284.12
Volume:  290.476
LogP:  1.82
LogD:  1.846
LogS:  -2.699
# Rotatable Bonds:  6
TPSA:  49.69
# H-Bond Aceptor:  3
# H-Bond Donor:  2
# Rings:  1
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.446
Synthetic Accessibility Score:  5.149
Fsp3:  0.6
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
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:  -4.514
MDCK Permeability:  3.476448546280153e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.005
Human Intestinal Absorption (HIA):  0.332
20% Bioavailability (F20%):  0.929
30% Bioavailability (F30%):  1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.837
Plasma Protein Binding (PPB):  58.89530944824219%
Volume Distribution (VD):  1.552
Pgp-substrate:  15.839401245117188%

ADMET: Metabolism

CYP1A2-inhibitor:  0.147
CYP1A2-substrate:  0.528
CYP2C19-inhibitor:  0.203
CYP2C19-substrate:  0.811
CYP2C9-inhibitor:  0.114
CYP2C9-substrate:  0.079
CYP2D6-inhibitor:  0.01
CYP2D6-substrate:  0.154
CYP3A4-inhibitor:  0.5
CYP3A4-substrate:  0.353

ADMET: Excretion

Clearance (CL):  11.936
Half-life (T1/2):  0.91

ADMET: Toxicity

hERG Blockers:  0.028
Human Hepatotoxicity (H-HT):  0.2
Drug-inuced Liver Injury (DILI):  0.417
AMES Toxicity:  0.319
Rat Oral Acute Toxicity:  0.554
Maximum Recommended Daily Dose:  0.853
Skin Sensitization:  0.886
Carcinogencity:  0.841
Eye Corrosion:  0.004
Eye Irritation:  0.171
Respiratory Toxicity:  0.965

Download Data

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

  Natural Product: NPC477422

Natural Product ID:  NPC477422
Common Name*:   (4Z,6R,7S,9S,12Z)-6,9-Epoxy-10-chloro-4,12-pentadecadiene-14-yne-3,7-diol
IUPAC Name:   (2R,3S,5S)-5-[(Z)-1-chlorohex-3-en-5-ynyl]-2-[(Z)-3-hydroxypent-1-enyl]oxolan-3-ol
Synonyms:  
Standard InCHIKey:  ABQCOYKPXJFCAW-FFHWLKLLSA-N
Standard InCHI:  InChI=1S/C15H21ClO3/c1-3-5-6-7-12(16)15-10-13(18)14(19-15)9-8-11(17)4-2/h1,5-6,8-9,11-15,17-18H,4,7,10H2,2H3/b6-5-,9-8-/t11?,12?,13-,14+,15-/m0/s1
SMILES:  CCC(/C=C\[C@@H]1[C@H](C[C@H](O1)C(C/C=C\C#C)Cl)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   25227559
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 NPC477422 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 NPC477421
0.7838 Intermediate Similarity NPC316572
0.7733 Intermediate Similarity NPC477423
0.7467 Intermediate Similarity NPC477431
0.7342 Intermediate Similarity NPC52781
0.7286 Intermediate Similarity NPC26310
0.7176 Intermediate Similarity NPC30915
0.7051 Intermediate Similarity NPC129630
0.6962 Remote Similarity NPC473306
0.6857 Remote Similarity NPC49059
0.6857 Remote Similarity NPC256209
0.6842 Remote Similarity NPC473722
0.6806 Remote Similarity NPC474577
0.6761 Remote Similarity NPC477726
0.6761 Remote Similarity NPC477725
0.6667 Remote Similarity NPC475384
0.6667 Remote Similarity NPC470968
0.6667 Remote Similarity NPC470967
0.6667 Remote Similarity NPC471960
0.6667 Remote Similarity NPC477661
0.6667 Remote Similarity NPC470969
0.6667 Remote Similarity NPC470966
0.6667 Remote Similarity NPC473847
0.6667 Remote Similarity NPC161838
0.6628 Remote Similarity NPC150502
0.6625 Remote Similarity NPC477429
0.6625 Remote Similarity NPC323677
0.6585 Remote Similarity NPC472174
0.6585 Remote Similarity NPC474280
0.6579 Remote Similarity NPC29697
0.6575 Remote Similarity NPC470970
0.6548 Remote Similarity NPC474278
0.6533 Remote Similarity NPC477430
0.6528 Remote Similarity NPC473725
0.6528 Remote Similarity NPC473896
0.6528 Remote Similarity NPC473735
0.6528 Remote Similarity NPC473721
0.6528 Remote Similarity NPC473910
0.6528 Remote Similarity NPC475353
0.6512 Remote Similarity NPC79367
0.6512 Remote Similarity NPC121374
0.65 Remote Similarity NPC472947
0.6494 Remote Similarity NPC475221
0.6471 Remote Similarity NPC248775
0.6456 Remote Similarity NPC25298
0.6447 Remote Similarity NPC66460
0.6447 Remote Similarity NPC271282
0.6447 Remote Similarity NPC325929
0.6444 Remote Similarity NPC477428
0.6429 Remote Similarity NPC151782
0.6429 Remote Similarity NPC93639
0.6429 Remote Similarity NPC29234
0.6429 Remote Similarity NPC129263
0.642 Remote Similarity NPC325098
0.641 Remote Similarity NPC19769
0.6395 Remote Similarity NPC475210
0.6395 Remote Similarity NPC470148
0.6395 Remote Similarity NPC476701
0.6395 Remote Similarity NPC1180
0.6395 Remote Similarity NPC470149
0.6395 Remote Similarity NPC473947
0.6395 Remote Similarity NPC180725
0.6395 Remote Similarity NPC477088
0.6389 Remote Similarity NPC473532
0.6389 Remote Similarity NPC110732
0.6386 Remote Similarity NPC471525
0.6386 Remote Similarity NPC24590
0.6374 Remote Similarity NPC477388
0.6374 Remote Similarity NPC477386
0.6364 Remote Similarity NPC474252
0.6353 Remote Similarity NPC474026
0.6329 Remote Similarity NPC201356
0.6329 Remote Similarity NPC276299
0.6322 Remote Similarity NPC91332
0.6322 Remote Similarity NPC133226
0.6322 Remote Similarity NPC470147
0.6322 Remote Similarity NPC162741
0.6316 Remote Similarity NPC469694
0.6316 Remote Similarity NPC258788
0.6316 Remote Similarity NPC471278
0.6316 Remote Similarity NPC477424
0.6296 Remote Similarity NPC475004
0.6296 Remote Similarity NPC130618
0.6286 Remote Similarity NPC72699
0.6279 Remote Similarity NPC28049
0.6279 Remote Similarity NPC473471
0.6265 Remote Similarity NPC470435
0.6265 Remote Similarity NPC329890
0.625 Remote Similarity NPC187361
0.625 Remote Similarity NPC477724
0.625 Remote Similarity NPC246621
0.625 Remote Similarity NPC34577
0.625 Remote Similarity NPC26102
0.625 Remote Similarity NPC474496
0.6235 Remote Similarity NPC301207
0.6235 Remote Similarity NPC209113
0.6235 Remote Similarity NPC190400
0.6235 Remote Similarity NPC236228
0.6235 Remote Similarity NPC127118
0.6235 Remote Similarity NPC256720
0.6235 Remote Similarity NPC49392
0.6234 Remote Similarity NPC475984
0.6203 Remote Similarity NPC96414
0.6197 Remote Similarity NPC59408
0.6197 Remote Similarity NPC71053
0.619 Remote Similarity NPC472173
0.6184 Remote Similarity NPC474267
0.6184 Remote Similarity NPC222852
0.6173 Remote Similarity NPC272961
0.6173 Remote Similarity NPC474823
0.6163 Remote Similarity NPC475711
0.6163 Remote Similarity NPC125365
0.6163 Remote Similarity NPC474818
0.6163 Remote Similarity NPC51809
0.6163 Remote Similarity NPC176329
0.6163 Remote Similarity NPC49302
0.6163 Remote Similarity NPC476703
0.6154 Remote Similarity NPC470965
0.6143 Remote Similarity NPC471275
0.6143 Remote Similarity NPC471280
0.6143 Remote Similarity NPC125122
0.6143 Remote Similarity NPC471276
0.6143 Remote Similarity NPC153538
0.6143 Remote Similarity NPC248884
0.6143 Remote Similarity NPC85079
0.6143 Remote Similarity NPC31194
0.6133 Remote Similarity NPC265551
0.6133 Remote Similarity NPC212730
0.6125 Remote Similarity NPC267027
0.6111 Remote Similarity NPC142092
0.6098 Remote Similarity NPC475982
0.6092 Remote Similarity NPC181838
0.6092 Remote Similarity NPC279214
0.6092 Remote Similarity NPC221095
0.6092 Remote Similarity NPC137345
0.6081 Remote Similarity NPC227135
0.6076 Remote Similarity NPC90463
0.6076 Remote Similarity NPC470320
0.6071 Remote Similarity NPC185186
0.6071 Remote Similarity NPC327383
0.6071 Remote Similarity NPC132938
0.6071 Remote Similarity NPC329914
0.6056 Remote Similarity NPC199286
0.6056 Remote Similarity NPC474642
0.6056 Remote Similarity NPC249670
0.6056 Remote Similarity NPC473913
0.6056 Remote Similarity NPC471281
0.6056 Remote Similarity NPC477727
0.6053 Remote Similarity NPC23418
0.6053 Remote Similarity NPC152438
0.6053 Remote Similarity NPC41180
0.6049 Remote Similarity NPC99619
0.6049 Remote Similarity NPC271921
0.6049 Remote Similarity NPC26500
0.6049 Remote Similarity NPC22101
0.6049 Remote Similarity NPC478097
0.6049 Remote Similarity NPC148192
0.6049 Remote Similarity NPC473752
0.6049 Remote Similarity NPC104537
0.6049 Remote Similarity NPC478100
0.6049 Remote Similarity NPC330426
0.6049 Remote Similarity NPC127091
0.6047 Remote Similarity NPC170148
0.6047 Remote Similarity NPC188860
0.6044 Remote Similarity NPC475732
0.6026 Remote Similarity NPC113293
0.6024 Remote Similarity NPC4299
0.6024 Remote Similarity NPC476037
0.6023 Remote Similarity NPC471537
0.6 Remote Similarity NPC310450
0.6 Remote Similarity NPC475046
0.6 Remote Similarity NPC478098
0.6 Remote Similarity NPC478099
0.6 Remote Similarity NPC11383
0.6 Remote Similarity NPC250836
0.6 Remote Similarity NPC470123
0.6 Remote Similarity NPC190859
0.6 Remote Similarity NPC474959
0.5981 Remote Similarity NPC35069
0.5981 Remote Similarity NPC258711
0.5977 Remote Similarity NPC233071
0.5976 Remote Similarity NPC63873
0.5976 Remote Similarity NPC324981
0.5976 Remote Similarity NPC473294
0.5976 Remote Similarity NPC48218
0.5976 Remote Similarity NPC475760
0.5976 Remote Similarity NPC473559
0.5976 Remote Similarity NPC141481
0.5976 Remote Similarity NPC471472
0.5974 Remote Similarity NPC122239
0.5974 Remote Similarity NPC473866
0.5972 Remote Similarity NPC170776
0.5972 Remote Similarity NPC294278
0.5972 Remote Similarity NPC200772
0.5972 Remote Similarity NPC475477
0.5972 Remote Similarity NPC55383
0.5972 Remote Similarity NPC256656
0.5972 Remote Similarity NPC473672
0.5972 Remote Similarity NPC224148
0.5972 Remote Similarity NPC474495

  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 NPC477422 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
0.6712 Remote Similarity NPD585 Clinical (unspecified phase)
0.6526 Remote Similarity NPD4792 Clinical (unspecified phase)
0.5604 Remote Similarity NPD5790 Clinical (unspecified phase)

  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