Structure

Physi-Chem Properties

Molecular Weight:  424.12
Volume:  401.841
LogP:  4.031
LogD:  3.76
LogS:  -4.705
# Rotatable Bonds:  12
TPSA:  63.6
# H-Bond Aceptor:  4
# H-Bond Donor:  1
# Rings:  1
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.221
Synthetic Accessibility Score:  3.796
Fsp3:  0.524
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.697
MDCK Permeability:  1.850931039371062e-05
Pgp-inhibitor:  0.999
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.169
20% Bioavailability (F20%):  0.017
30% Bioavailability (F30%):  0.951

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.95
Plasma Protein Binding (PPB):  98.32266998291016%
Volume Distribution (VD):  1.431
Pgp-substrate:  1.3808484077453613%

ADMET: Metabolism

CYP1A2-inhibitor:  0.938
CYP1A2-substrate:  0.715
CYP2C19-inhibitor:  0.951
CYP2C19-substrate:  0.711
CYP2C9-inhibitor:  0.902
CYP2C9-substrate:  0.918
CYP2D6-inhibitor:  0.817
CYP2D6-substrate:  0.319
CYP3A4-inhibitor:  0.939
CYP3A4-substrate:  0.439

ADMET: Excretion

Clearance (CL):  1.943
Half-life (T1/2):  0.876

ADMET: Toxicity

hERG Blockers:  0.263
Human Hepatotoxicity (H-HT):  0.733
Drug-inuced Liver Injury (DILI):  0.201
AMES Toxicity:  0.838
Rat Oral Acute Toxicity:  0.61
Maximum Recommended Daily Dose:  0.885
Skin Sensitization:  0.972
Carcinogencity:  0.864
Eye Corrosion:  0.005
Eye Irritation:  0.104
Respiratory Toxicity:  0.938

Download Data

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

  Natural Product: NPC63326

Natural Product ID:  NPC63326
Common Name*:   Bromoclavulone Iii
IUPAC Name:   methyl (E,7Z)-7-[(2R)-4-bromo-2-hydroxy-2-[(Z)-oct-2-enyl]-5-oxocyclopent-3-en-1-ylidene]hept-5-enoate
Synonyms:   Bromoclavulone Iii
Standard InCHIKey:  SEUGRXZAXYVQIH-MNSXJSHLSA-N
Standard InCHI:  InChI=1S/C21H29BrO4/c1-3-4-5-6-9-12-15-21(25)16-18(22)20(24)17(21)13-10-7-8-11-14-19(23)26-2/h7,9-10,12-13,16,25H,3-6,8,11,14-15H2,1-2H3/b10-7+,12-9-,17-13+/t21-/m1/s1
SMILES:  CCCCC/C=CC[C@@]1(O)C=C(C(=O)/C/1=CC=CCCCC(=O)OC)Br
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL513465
PubChem CID:   10432521
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003909] Fatty Acyls
        • [CHEMONTID:0000513] Eicosanoids
          • [CHEMONTID:0001021] Clavulones and derivatives

*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
NPO3077 Clavularia viridis Species Clavulariidae Eukaryota n.a. Okinawan n.a. PMID[11720524]
NPO3077 Clavularia viridis Species Clavulariidae Eukaryota n.a. Formosan soft corals n.a. PMID[12444673]
NPO3077 Clavularia viridis Species Clavulariidae Eukaryota n.a. Taiwanese octocoral n.a. PMID[15104481]
NPO3077 Clavularia viridis Species Clavulariidae 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
NPT306 Cell Line PC-3 Homo sapiens IC50 = 500.0 nM PMID[448427]
NPT139 Cell Line HT-29 Homo sapiens IC50 = 500.0 nM PMID[448427]

☑ 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 NPC63326 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
1.0 High Similarity NPC265980
0.9178 High Similarity NPC12815
0.9178 High Similarity NPC238948
0.9178 High Similarity NPC215745
0.8816 High Similarity NPC51391
0.8816 High Similarity NPC4492
0.8182 Intermediate Similarity NPC287878
0.7703 Intermediate Similarity NPC322457
0.7529 Intermediate Similarity NPC26624
0.7375 Intermediate Similarity NPC319163
0.7375 Intermediate Similarity NPC67076
0.7342 Intermediate Similarity NPC473603
0.7342 Intermediate Similarity NPC236208
0.7342 Intermediate Similarity NPC476059
0.725 Intermediate Similarity NPC318766
0.7241 Intermediate Similarity NPC16488
0.7209 Intermediate Similarity NPC474980
0.7195 Intermediate Similarity NPC122244
0.7191 Intermediate Similarity NPC315395
0.7191 Intermediate Similarity NPC316426
0.716 Intermediate Similarity NPC106309
0.7111 Intermediate Similarity NPC72513
0.7108 Intermediate Similarity NPC260396
0.7105 Intermediate Similarity NPC64985
0.7093 Intermediate Similarity NPC160582
0.7079 Intermediate Similarity NPC125290
0.7059 Intermediate Similarity NPC279532
0.7013 Intermediate Similarity NPC190049
0.6988 Remote Similarity NPC227396
0.6951 Remote Similarity NPC316185
0.6932 Remote Similarity NPC85772
0.6914 Remote Similarity NPC470693
0.6905 Remote Similarity NPC169056
0.6905 Remote Similarity NPC166018
0.6905 Remote Similarity NPC225665
0.6905 Remote Similarity NPC68624
0.6889 Remote Similarity NPC261380
0.6875 Remote Similarity NPC21998
0.686 Remote Similarity NPC192006
0.686 Remote Similarity NPC93763
0.686 Remote Similarity NPC267231
0.686 Remote Similarity NPC476627
0.686 Remote Similarity NPC108816
0.6854 Remote Similarity NPC161045
0.6849 Remote Similarity NPC474127
0.6849 Remote Similarity NPC322461
0.6848 Remote Similarity NPC26078
0.6848 Remote Similarity NPC473658
0.6842 Remote Similarity NPC86789
0.6835 Remote Similarity NPC470688
0.6824 Remote Similarity NPC203277
0.6818 Remote Similarity NPC325031
0.6813 Remote Similarity NPC234038
0.6809 Remote Similarity NPC32552
0.6809 Remote Similarity NPC111114
0.6809 Remote Similarity NPC180617
0.6809 Remote Similarity NPC142838
0.6809 Remote Similarity NPC300312
0.6809 Remote Similarity NPC261607
0.6795 Remote Similarity NPC68110
0.6786 Remote Similarity NPC315843
0.6786 Remote Similarity NPC470686
0.6786 Remote Similarity NPC476590
0.6786 Remote Similarity NPC114727
0.6782 Remote Similarity NPC472013
0.6782 Remote Similarity NPC476624
0.6778 Remote Similarity NPC219966
0.6774 Remote Similarity NPC307092
0.6774 Remote Similarity NPC51358
0.675 Remote Similarity NPC308294
0.675 Remote Similarity NPC142423
0.6747 Remote Similarity NPC288667
0.6747 Remote Similarity NPC293114
0.6747 Remote Similarity NPC126061
0.6742 Remote Similarity NPC8161
0.6737 Remote Similarity NPC29798
0.6737 Remote Similarity NPC282644
0.6707 Remote Similarity NPC67608
0.6707 Remote Similarity NPC143396
0.6707 Remote Similarity NPC473277
0.6706 Remote Similarity NPC329852
0.6706 Remote Similarity NPC161038
0.6703 Remote Similarity NPC11804
0.6703 Remote Similarity NPC470755
0.6702 Remote Similarity NPC475879
0.6667 Remote Similarity NPC182292
0.6667 Remote Similarity NPC325977
0.6667 Remote Similarity NPC153660
0.6667 Remote Similarity NPC153570
0.6667 Remote Similarity NPC264391
0.6667 Remote Similarity NPC263732
0.6667 Remote Similarity NPC260343
0.6667 Remote Similarity NPC248624
0.6667 Remote Similarity NPC167219
0.6667 Remote Similarity NPC106613
0.6633 Remote Similarity NPC245521
0.6632 Remote Similarity NPC472705
0.663 Remote Similarity NPC291712
0.663 Remote Similarity NPC261721
0.6628 Remote Similarity NPC225022
0.6628 Remote Similarity NPC16279
0.6628 Remote Similarity NPC256640
0.6628 Remote Similarity NPC238554
0.6628 Remote Similarity NPC205615
0.6627 Remote Similarity NPC203819
0.6627 Remote Similarity NPC67183
0.6625 Remote Similarity NPC220766
0.6623 Remote Similarity NPC329249
0.6623 Remote Similarity NPC318306
0.66 Remote Similarity NPC469851
0.6598 Remote Similarity NPC209355
0.6596 Remote Similarity NPC36668
0.6596 Remote Similarity NPC212598
0.6596 Remote Similarity NPC87306
0.6596 Remote Similarity NPC118011
0.6593 Remote Similarity NPC196487
0.6593 Remote Similarity NPC158756
0.6593 Remote Similarity NPC14575
0.6591 Remote Similarity NPC99651
0.6591 Remote Similarity NPC164308
0.6588 Remote Similarity NPC107654
0.6588 Remote Similarity NPC177030
0.6585 Remote Similarity NPC470256
0.6585 Remote Similarity NPC476614
0.6585 Remote Similarity NPC309466
0.6582 Remote Similarity NPC155849
0.6579 Remote Similarity NPC283502
0.6559 Remote Similarity NPC160138
0.6559 Remote Similarity NPC473248
0.6559 Remote Similarity NPC471738
0.6552 Remote Similarity NPC228902
0.6552 Remote Similarity NPC320630
0.6552 Remote Similarity NPC97173
0.6552 Remote Similarity NPC275530
0.6552 Remote Similarity NPC116177
0.6552 Remote Similarity NPC82666
0.6552 Remote Similarity NPC472014
0.6552 Remote Similarity NPC7563
0.6552 Remote Similarity NPC24827
0.6543 Remote Similarity NPC191233
0.6543 Remote Similarity NPC146811
0.6526 Remote Similarity NPC473455
0.6526 Remote Similarity NPC179394
0.6526 Remote Similarity NPC144133
0.6526 Remote Similarity NPC77337
0.6522 Remote Similarity NPC281172
0.6522 Remote Similarity NPC307112
0.6522 Remote Similarity NPC476628
0.6517 Remote Similarity NPC115418
0.6512 Remote Similarity NPC478191
0.6512 Remote Similarity NPC478194
0.6512 Remote Similarity NPC478196
0.6512 Remote Similarity NPC478193
0.6512 Remote Similarity NPC478195
0.6512 Remote Similarity NPC478192
0.6506 Remote Similarity NPC88877
0.6506 Remote Similarity NPC475982
0.6506 Remote Similarity NPC476591
0.6506 Remote Similarity NPC151481
0.6494 Remote Similarity NPC471619
0.6489 Remote Similarity NPC476805
0.6489 Remote Similarity NPC475819
0.6489 Remote Similarity NPC72397
0.6484 Remote Similarity NPC169575
0.6484 Remote Similarity NPC475083
0.6484 Remote Similarity NPC40746
0.6484 Remote Similarity NPC250315
0.6477 Remote Similarity NPC253749
0.6477 Remote Similarity NPC315765
0.6477 Remote Similarity NPC478122
0.6477 Remote Similarity NPC169095
0.6471 Remote Similarity NPC284006
0.6463 Remote Similarity NPC194871
0.6463 Remote Similarity NPC203335
0.6458 Remote Similarity NPC474018
0.6458 Remote Similarity NPC473986
0.6458 Remote Similarity NPC193396
0.6458 Remote Similarity NPC32944
0.6456 Remote Similarity NPC40082
0.6456 Remote Similarity NPC151648
0.6452 Remote Similarity NPC472009
0.6452 Remote Similarity NPC469910
0.6452 Remote Similarity NPC122502
0.6447 Remote Similarity NPC472808
0.6447 Remote Similarity NPC324224
0.6444 Remote Similarity NPC59994
0.6444 Remote Similarity NPC275766
0.6444 Remote Similarity NPC42470
0.6444 Remote Similarity NPC275507
0.6444 Remote Similarity NPC112868
0.6444 Remote Similarity NPC78677
0.6438 Remote Similarity NPC43053
0.6437 Remote Similarity NPC68819
0.6436 Remote Similarity NPC206079
0.6429 Remote Similarity NPC59558
0.6429 Remote Similarity NPC472017
0.6429 Remote Similarity NPC214694
0.6429 Remote Similarity NPC315597
0.6429 Remote Similarity NPC315285
0.6421 Remote Similarity NPC106040

  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 NPC63326 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
0.6932 Remote Similarity NPD5209 Approved
0.6744 Remote Similarity NPD4756 Discovery
0.6703 Remote Similarity NPD5363 Approved
0.6526 Remote Similarity NPD5785 Approved
0.6517 Remote Similarity NPD4252 Approved
0.6374 Remote Similarity NPD4270 Approved
0.6374 Remote Similarity NPD4269 Approved
0.6329 Remote Similarity NPD4246 Clinical (unspecified phase)
0.6304 Remote Similarity NPD5362 Discontinued
0.6304 Remote Similarity NPD7154 Phase 3
0.6277 Remote Similarity NPD5786 Approved
0.6265 Remote Similarity NPD4247 Clinical (unspecified phase)
0.6264 Remote Similarity NPD5369 Approved
0.6164 Remote Similarity NPD4220 Pre-registration
0.6154 Remote Similarity NPD4820 Approved
0.6154 Remote Similarity NPD4822 Approved
0.6154 Remote Similarity NPD4819 Approved
0.6154 Remote Similarity NPD4821 Approved
0.6154 Remote Similarity NPD5790 Clinical (unspecified phase)
0.6122 Remote Similarity NPD7983 Approved
0.6122 Remote Similarity NPD7637 Suspended
0.6111 Remote Similarity NPD4271 Approved
0.6111 Remote Similarity NPD5784 Clinical (unspecified phase)
0.6111 Remote Similarity NPD4268 Approved
0.61 Remote Similarity NPD1698 Clinical (unspecified phase)
0.6082 Remote Similarity NPD5370 Suspended
0.6061 Remote Similarity NPD5778 Approved
0.6061 Remote Similarity NPD5779 Approved
0.6049 Remote Similarity NPD4191 Approved
0.6049 Remote Similarity NPD4193 Approved
0.6049 Remote Similarity NPD4194 Approved
0.6049 Remote Similarity NPD4192 Approved
0.6 Remote Similarity NPD6647 Phase 2
0.6 Remote Similarity NPD1696 Phase 3
0.596 Remote Similarity NPD4810 Clinical (unspecified phase)
0.5957 Remote Similarity NPD5332 Approved
0.5957 Remote Similarity NPD5331 Approved
0.5922 Remote Similarity NPD8029 Clinical (unspecified phase)
0.5914 Remote Similarity NPD4790 Discontinued
0.5882 Remote Similarity NPD7839 Suspended
0.5859 Remote Similarity NPD7838 Discovery
0.5833 Remote Similarity NPD2685 Clinical (unspecified phase)
0.5818 Remote Similarity NPD6371 Approved
0.5806 Remote Similarity NPD8259 Clinical (unspecified phase)
0.5773 Remote Similarity NPD4249 Approved
0.5769 Remote Similarity NPD4225 Approved
0.5765 Remote Similarity NPD7331 Phase 2
0.5758 Remote Similarity NPD5764 Clinical (unspecified phase)
0.5758 Remote Similarity NPD6101 Approved
0.5753 Remote Similarity NPD4222 Approved
0.5733 Remote Similarity NPD3173 Approved
0.5729 Remote Similarity NPD6400 Clinical (unspecified phase)
0.5714 Remote Similarity NPD4251 Approved
0.5714 Remote Similarity NPD4250 Approved
0.5688 Remote Similarity NPD7899 Clinical (unspecified phase)
0.5686 Remote Similarity NPD5282 Discontinued
0.5644 Remote Similarity NPD5281 Approved
0.5644 Remote Similarity NPD5284 Approved
0.5644 Remote Similarity NPD6411 Approved
0.5625 Remote Similarity NPD6110 Phase 1
0.5625 Remote Similarity NPD7601 Clinical (unspecified phase)
0.5612 Remote Similarity NPD4623 Approved
0.5612 Remote Similarity NPD4519 Discontinued
0.5604 Remote Similarity NPD8039 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