Structure

Physi-Chem Properties

Molecular Weight:  408.03
Volume:  332.796
LogP:  3.506
LogD:  3.213
LogS:  -3.954
# Rotatable Bonds:  3
TPSA:  57.29
# H-Bond Aceptor:  5
# H-Bond Donor:  0
# Rings:  3
# Heavy Atoms:  7

MedChem Properties

QED Drug-Likeness Score:  0.304
Synthetic Accessibility Score:  6.299
Fsp3:  0.812
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.742
MDCK Permeability:  4.533932587946765e-05
Pgp-inhibitor:  0.681
Pgp-substrate:  0.002
Human Intestinal Absorption (HIA):  0.004
20% Bioavailability (F20%):  0.006
30% Bioavailability (F30%):  0.447

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.639
Plasma Protein Binding (PPB):  88.50140380859375%
Volume Distribution (VD):  2.033
Pgp-substrate:  3.8512401580810547%

ADMET: Metabolism

CYP1A2-inhibitor:  0.08
CYP1A2-substrate:  0.615
CYP2C19-inhibitor:  0.25
CYP2C19-substrate:  0.902
CYP2C9-inhibitor:  0.434
CYP2C9-substrate:  0.039
CYP2D6-inhibitor:  0.004
CYP2D6-substrate:  0.421
CYP3A4-inhibitor:  0.641
CYP3A4-substrate:  0.791

ADMET: Excretion

Clearance (CL):  5.873
Half-life (T1/2):  0.43

ADMET: Toxicity

hERG Blockers:  0.846
Human Hepatotoxicity (H-HT):  0.422
Drug-inuced Liver Injury (DILI):  0.899
AMES Toxicity:  0.364
Rat Oral Acute Toxicity:  0.093
Maximum Recommended Daily Dose:  0.669
Skin Sensitization:  0.95
Carcinogencity:  0.567
Eye Corrosion:  0.126
Eye Irritation:  0.101
Respiratory Toxicity:  0.974

Download Data

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

  Natural Product: NPC477428

Natural Product ID:  NPC477428
Common Name*:   methyl (Z)-3-[(1S,2S,4R,6R,7S,9R,11R,12R)-2-bromo-12-chloro-7-methyl-5,8,14-trioxatricyclo[9.2.1.04,6]tetradecan-9-yl]prop-2-enoate
IUPAC Name:   methyl (Z)-3-[(1S,2S,4R,6R,7S,9R,11R,12R)-2-bromo-12-chloro-7-methyl-5,8,14-trioxatricyclo[9.2.1.04,6]tetradecan-9-yl]prop-2-enoate
Synonyms:  
Standard InCHIKey:  NZBKCNQQOBHOFJ-MWLCHPCFSA-N
Standard InCHI:  InChI=1S/C16H22BrClO5/c1-8-16-14(23-16)6-10(17)12-7-11(18)13(22-12)5-9(21-8)3-4-15(19)20-2/h3-4,8-14,16H,5-7H2,1-2H3/b4-3-/t8-,9-,10-,11+,12-,13+,14+,16+/m0/s1
SMILES:  C[C@H]1[C@@H]2[C@H](O2)C[C@@H]([C@@H]3C[C@H]([C@H](O3)C[C@@H](O1)/C=C\C(=O)OC)Cl)Br
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   54582321
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003909] Fatty Acyls
        • [CHEMONTID:0000324] Fatty acid esters

*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
NPO30005 Laurencia marilzae Species Rhodomelaceae Eukaryota n.a. n.a. n.a. PMID[21338119]
NPO30005 Laurencia marilzae Species Rhodomelaceae Eukaryota n.a. Paraso Floral, Tenerife, Canary Islands n.a. PMID[21338119]

☑ 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
NPT179 Cell Line A2780 Homo sapiens GI50 > 10 ug/ml PMID[21338119]
NPT1723 Cell Line HBL-100 Homo sapiens GI50 > 10 ug/ml PMID[21338119]
NPT165 Cell Line HeLa Homo sapiens GI50 > 10 ug/ml PMID[21338119]
NPT1577 Cell Line SW1573 Homo sapiens GI50 > 10 ug/ml PMID[21338119]
NPT396 Cell Line T47D Homo sapiens GI50 > 10 ug/ml PMID[21338119]
NPT1183 Cell Line WiDr Homo sapiens GI50 > 10 ug/ml PMID[21338119]

☑ 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 NPC477428 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
0.8 Intermediate Similarity NPC473947
0.7901 Intermediate Similarity NPC325098
0.7654 Intermediate Similarity NPC477431
0.7529 Intermediate Similarity NPC477421
0.747 Intermediate Similarity NPC323677
0.747 Intermediate Similarity NPC477423
0.747 Intermediate Similarity NPC477429
0.7381 Intermediate Similarity NPC475762
0.7326 Intermediate Similarity NPC52781
0.7024 Intermediate Similarity NPC475760
0.6966 Remote Similarity NPC233071
0.6966 Remote Similarity NPC474026
0.6889 Remote Similarity NPC248775
0.6854 Remote Similarity NPC188860
0.6813 Remote Similarity NPC470148
0.6813 Remote Similarity NPC470149
0.6813 Remote Similarity NPC180725
0.6786 Remote Similarity NPC124586
0.6747 Remote Similarity NPC308457
0.6739 Remote Similarity NPC470147
0.6739 Remote Similarity NPC133226
0.6705 Remote Similarity NPC185186
0.6705 Remote Similarity NPC327383
0.6705 Remote Similarity NPC329914
0.6632 Remote Similarity NPC30915
0.663 Remote Similarity NPC1180
0.6593 Remote Similarity NPC475711
0.6591 Remote Similarity NPC473306
0.6562 Remote Similarity NPC471567
0.6562 Remote Similarity NPC322529
0.6562 Remote Similarity NPC120398
0.6556 Remote Similarity NPC285840
0.6556 Remote Similarity NPC327041
0.6548 Remote Similarity NPC148233
0.6548 Remote Similarity NPC25747
0.6517 Remote Similarity NPC329890
0.6495 Remote Similarity NPC204048
0.6489 Remote Similarity NPC473339
0.6489 Remote Similarity NPC471552
0.6489 Remote Similarity NPC469469
0.6477 Remote Similarity NPC476012
0.6465 Remote Similarity NPC133450
0.6458 Remote Similarity NPC186155
0.6458 Remote Similarity NPC163093
0.6458 Remote Similarity NPC156804
0.6458 Remote Similarity NPC160517
0.6458 Remote Similarity NPC78673
0.6452 Remote Similarity NPC477088
0.6444 Remote Similarity NPC477422
0.6444 Remote Similarity NPC77724
0.6429 Remote Similarity NPC231889
0.64 Remote Similarity NPC177668
0.64 Remote Similarity NPC475748
0.64 Remote Similarity NPC3952
0.6392 Remote Similarity NPC329615
0.6392 Remote Similarity NPC477014
0.6392 Remote Similarity NPC477013
0.6392 Remote Similarity NPC329838
0.6389 Remote Similarity NPC166115
0.6386 Remote Similarity NPC26223
0.6383 Remote Similarity NPC474739
0.6373 Remote Similarity NPC473330
0.6373 Remote Similarity NPC473316
0.6364 Remote Similarity NPC316572
0.6364 Remote Similarity NPC89001
0.6364 Remote Similarity NPC20339
0.6364 Remote Similarity NPC40376
0.6364 Remote Similarity NPC473905
0.6364 Remote Similarity NPC233551
0.6364 Remote Similarity NPC48338
0.6364 Remote Similarity NPC320458
0.6364 Remote Similarity NPC280621
0.6364 Remote Similarity NPC21208
0.6354 Remote Similarity NPC170286
0.6354 Remote Similarity NPC253801
0.6339 Remote Similarity NPC35069
0.6339 Remote Similarity NPC95290
0.6339 Remote Similarity NPC189338
0.6339 Remote Similarity NPC258711
0.6327 Remote Similarity NPC208473
0.6327 Remote Similarity NPC171174
0.6327 Remote Similarity NPC477015
0.6327 Remote Similarity NPC309211
0.6327 Remote Similarity NPC232555
0.6327 Remote Similarity NPC231096
0.6327 Remote Similarity NPC61527
0.6327 Remote Similarity NPC62118
0.6327 Remote Similarity NPC240695
0.6327 Remote Similarity NPC50637
0.6327 Remote Similarity NPC279267
0.6327 Remote Similarity NPC475581
0.6327 Remote Similarity NPC142117
0.6327 Remote Similarity NPC114694
0.6327 Remote Similarity NPC241360
0.6327 Remote Similarity NPC293136
0.6327 Remote Similarity NPC132940
0.6327 Remote Similarity NPC69082
0.6327 Remote Similarity NPC107717
0.63 Remote Similarity NPC477016
0.63 Remote Similarity NPC166919
0.63 Remote Similarity NPC151770
0.63 Remote Similarity NPC477017
0.6292 Remote Similarity NPC476037
0.6283 Remote Similarity NPC273242
0.6277 Remote Similarity NPC139712
0.6277 Remote Similarity NPC226226
0.6277 Remote Similarity NPC55304
0.6265 Remote Similarity NPC22897
0.6265 Remote Similarity NPC159650
0.6265 Remote Similarity NPC474267
0.6264 Remote Similarity NPC477204
0.6263 Remote Similarity NPC178215
0.6263 Remote Similarity NPC20533
0.6263 Remote Similarity NPC258068
0.6263 Remote Similarity NPC476583
0.625 Remote Similarity NPC73310
0.625 Remote Similarity NPC218477
0.625 Remote Similarity NPC473780
0.625 Remote Similarity NPC180363
0.625 Remote Similarity NPC473529
0.625 Remote Similarity NPC131002
0.625 Remote Similarity NPC329829
0.625 Remote Similarity NPC11332
0.625 Remote Similarity NPC94875
0.625 Remote Similarity NPC279621
0.625 Remote Similarity NPC471472
0.625 Remote Similarity NPC145914
0.625 Remote Similarity NPC473294
0.625 Remote Similarity NPC475159
0.625 Remote Similarity NPC65930
0.625 Remote Similarity NPC473712
0.6238 Remote Similarity NPC471569
0.6238 Remote Similarity NPC239517
0.6228 Remote Similarity NPC121816
0.6224 Remote Similarity NPC132496
0.6224 Remote Similarity NPC469570
0.6224 Remote Similarity NPC231009
0.6224 Remote Similarity NPC82795
0.6224 Remote Similarity NPC235809
0.6224 Remote Similarity NPC25764
0.6224 Remote Similarity NPC66346
0.6224 Remote Similarity NPC319036
0.6224 Remote Similarity NPC103284
0.6224 Remote Similarity NPC39279
0.6224 Remote Similarity NPC1083
0.6224 Remote Similarity NPC473669
0.6224 Remote Similarity NPC9678
0.6224 Remote Similarity NPC223871
0.6224 Remote Similarity NPC292809
0.6224 Remote Similarity NPC473478
0.6224 Remote Similarity NPC202055
0.6224 Remote Similarity NPC473156
0.6224 Remote Similarity NPC39167
0.6224 Remote Similarity NPC48210
0.6224 Remote Similarity NPC477018
0.6224 Remote Similarity NPC283085
0.6224 Remote Similarity NPC107986
0.6224 Remote Similarity NPC110710
0.6224 Remote Similarity NPC100921
0.6224 Remote Similarity NPC286338
0.6224 Remote Similarity NPC470400
0.6224 Remote Similarity NPC473671
0.6224 Remote Similarity NPC473651
0.6224 Remote Similarity NPC475268
0.6224 Remote Similarity NPC77871
0.6222 Remote Similarity NPC477084
0.6214 Remote Similarity NPC471147
0.6214 Remote Similarity NPC256368
0.6211 Remote Similarity NPC474510
0.6207 Remote Similarity NPC248125
0.6207 Remote Similarity NPC276299
0.62 Remote Similarity NPC234077
0.62 Remote Similarity NPC39754
0.62 Remote Similarity NPC171135
0.62 Remote Similarity NPC172821
0.62 Remote Similarity NPC287164
0.62 Remote Similarity NPC100454
0.62 Remote Similarity NPC81045
0.62 Remote Similarity NPC191929
0.62 Remote Similarity NPC169511
0.62 Remote Similarity NPC242364
0.62 Remote Similarity NPC261952
0.62 Remote Similarity NPC151403
0.62 Remote Similarity NPC61257
0.62 Remote Similarity NPC274446
0.62 Remote Similarity NPC320569
0.62 Remote Similarity NPC133730
0.619 Remote Similarity NPC245521
0.6186 Remote Similarity NPC231601
0.6186 Remote Similarity NPC144415
0.6182 Remote Similarity NPC319438
0.618 Remote Similarity NPC269841
0.6176 Remote Similarity NPC158061
0.6174 Remote Similarity NPC170692
0.6174 Remote Similarity NPC255450
0.6162 Remote Similarity NPC112685
0.6162 Remote Similarity NPC282815
0.6162 Remote Similarity NPC219652
0.6162 Remote Similarity NPC134807
0.6162 Remote Similarity NPC25703

  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 NPC477428 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
0.64 Remote Similarity NPD7838 Discovery
0.6092 Remote Similarity NPD2685 Clinical (unspecified phase)
0.6078 Remote Similarity NPD6698 Approved
0.6078 Remote Similarity NPD46 Approved
0.6061 Remote Similarity NPD1733 Clinical (unspecified phase)
0.5926 Remote Similarity NPD6648 Approved
0.5872 Remote Similarity NPD5344 Discontinued
0.5794 Remote Similarity NPD4792 Clinical (unspecified phase)
0.5673 Remote Similarity NPD1695 Approved
0.56 Remote Similarity NPD5209 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