Structure

Physi-Chem Properties

Molecular Weight:  258.16
Volume:  301.713
LogP:  5.153
LogD:  2.946
LogS:  -4.799
# Rotatable Bonds:  8
TPSA:  37.3
# H-Bond Aceptor:  2
# H-Bond Donor:  1
# Rings:  0
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.407
Synthetic Accessibility Score:  3.452
Fsp3:  0.529
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.754
MDCK Permeability:  3.725504575413652e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.011
20% Bioavailability (F20%):  0.012
30% Bioavailability (F30%):  0.786

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.01
Plasma Protein Binding (PPB):  100.6355209350586%
Volume Distribution (VD):  0.623
Pgp-substrate:  0.835699200630188%

ADMET: Metabolism

CYP1A2-inhibitor:  0.083
CYP1A2-substrate:  0.287
CYP2C19-inhibitor:  0.726
CYP2C19-substrate:  0.55
CYP2C9-inhibitor:  0.495
CYP2C9-substrate:  0.993
CYP2D6-inhibitor:  0.005
CYP2D6-substrate:  0.06
CYP3A4-inhibitor:  0.366
CYP3A4-substrate:  0.023

ADMET: Excretion

Clearance (CL):  1.835
Half-life (T1/2):  0.851

ADMET: Toxicity

hERG Blockers:  0.018
Human Hepatotoxicity (H-HT):  0.936
Drug-inuced Liver Injury (DILI):  0.971
AMES Toxicity:  0.368
Rat Oral Acute Toxicity:  0.178
Maximum Recommended Daily Dose:  0.407
Skin Sensitization:  0.971
Carcinogencity:  0.634
Eye Corrosion:  0.972
Eye Irritation:  0.975
Respiratory Toxicity:  0.951

Download Data

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

  Natural Product: NPC470410

Natural Product ID:  NPC470410
Common Name*:   Phomallenic Acid B
IUPAC Name:   heptadeca-8,9-dien-11,13-diynoic acid
Synonyms:  
Standard InCHIKey:  VMBBTKBMFHKNCM-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C17H22O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17(18)19/h8,10H,2-3,11-16H2,1H3,(H,18,19)
SMILES:  CCCC#CC#CC=C=CCCCCCCC(=O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2028079
PubChem CID:   11680457
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003909] Fatty Acyls
        • [CHEMONTID:0000262] Fatty acids and conjugates
          • [CHEMONTID:0002949] Long-chain fatty acids

*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
NPO32661 Phoma sp. Species Didymellaceae Eukaryota n.a. n.a. n.a. PMID[16562839]
NPO32661 Phoma sp. Species Didymellaceae Eukaryota n.a. n.a. n.a. PMID[16643061]
NPO32661 Phoma sp. Species Didymellaceae Eukaryota giant jellyfish Nemopilema nomurai n.a. n.a. PMID[22483395]
NPO32661 Phoma sp. Species Didymellaceae Eukaryota n.a. n.a. n.a. PMID[26651221]
NPO32661 Phoma sp. Species Didymellaceae Eukaryota n.a. n.a. n.a. PMID[30785282]
NPO32661 Phoma sp. Species Didymellaceae Eukaryota n.a. n.a. n.a. PMID[31120749]
NPO32661 Phoma sp. Species Didymellaceae Eukaryota n.a. n.a. n.a. PMID[7561907]

☑ 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
NPT16 Organism Staphylococcus aureus Staphylococcus aureus Activity = 0.31 ug ml-1 PMID[535822]
NPT2 Others Unspecified IC50 = 3.4 ug.mL-1 PMID[535822]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC = 7.8 ug.mL-1 PMID[535822]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC = 12.5 ug.mL-1 PMID[535822]
NPT175 Organism Enterococcus faecalis Enterococcus faecalis MIC > 100.0 ug.mL-1 PMID[535822]
NPT1531 Organism Enterococcus faecium Enterococcus faecium MIC > 100.0 ug.mL-1 PMID[535822]
NPT19 Organism Escherichia coli Escherichia coli MIC > 100.0 ug.mL-1 PMID[535822]
NPT19 Organism Escherichia coli Escherichia coli MIC = 25.0 ug.mL-1 PMID[535822]

☑ 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 NPC470410 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 NPC470412
0.9388 High Similarity NPC18357
0.9038 High Similarity NPC187777
0.9038 High Similarity NPC179764
0.8846 High Similarity NPC274290
0.8846 High Similarity NPC473863
0.8846 High Similarity NPC54766
0.8627 High Similarity NPC161366
0.8571 High Similarity NPC180534
0.8519 High Similarity NPC225929
0.8511 High Similarity NPC255837
0.8511 High Similarity NPC19305
0.8462 Intermediate Similarity NPC1813
0.8462 Intermediate Similarity NPC294548
0.8462 Intermediate Similarity NPC139029
0.8462 Intermediate Similarity NPC36061
0.8333 Intermediate Similarity NPC8219
0.8302 Intermediate Similarity NPC85813
0.8302 Intermediate Similarity NPC290563
0.8302 Intermediate Similarity NPC281972
0.8302 Intermediate Similarity NPC154245
0.8302 Intermediate Similarity NPC424
0.8302 Intermediate Similarity NPC25417
0.8302 Intermediate Similarity NPC87564
0.8302 Intermediate Similarity NPC32467
0.8302 Intermediate Similarity NPC88966
0.8302 Intermediate Similarity NPC261831
0.8302 Intermediate Similarity NPC6095
0.8269 Intermediate Similarity NPC281245
0.8113 Intermediate Similarity NPC321062
0.8113 Intermediate Similarity NPC70387
0.8085 Intermediate Similarity NPC103286
0.8085 Intermediate Similarity NPC163746
0.8077 Intermediate Similarity NPC28205
0.8077 Intermediate Similarity NPC470411
0.8077 Intermediate Similarity NPC284212
0.807 Intermediate Similarity NPC235242
0.8036 Intermediate Similarity NPC267817
0.8 Intermediate Similarity NPC477201
0.8 Intermediate Similarity NPC18951
0.7925 Intermediate Similarity NPC92114
0.7917 Intermediate Similarity NPC301528
0.7917 Intermediate Similarity NPC129972
0.7917 Intermediate Similarity NPC71317
0.7885 Intermediate Similarity NPC224227
0.7843 Intermediate Similarity NPC216130
0.7736 Intermediate Similarity NPC262968
0.7708 Intermediate Similarity NPC149184
0.7708 Intermediate Similarity NPC307783
0.7708 Intermediate Similarity NPC196924
0.7708 Intermediate Similarity NPC209970
0.7708 Intermediate Similarity NPC171736
0.7708 Intermediate Similarity NPC216630
0.7692 Intermediate Similarity NPC149821
0.7692 Intermediate Similarity NPC5413
0.7692 Intermediate Similarity NPC304162
0.7667 Intermediate Similarity NPC226592
0.7667 Intermediate Similarity NPC470320
0.766 Intermediate Similarity NPC113928
0.766 Intermediate Similarity NPC201844
0.766 Intermediate Similarity NPC261080
0.766 Intermediate Similarity NPC154186
0.766 Intermediate Similarity NPC279026
0.766 Intermediate Similarity NPC14227
0.766 Intermediate Similarity NPC301585
0.766 Intermediate Similarity NPC301696
0.7636 Intermediate Similarity NPC87394
0.7586 Intermediate Similarity NPC274927
0.7586 Intermediate Similarity NPC106851
0.7551 Intermediate Similarity NPC67462
0.7547 Intermediate Similarity NPC59051
0.75 Intermediate Similarity NPC45626
0.75 Intermediate Similarity NPC207292
0.7458 Intermediate Similarity NPC251042
0.7458 Intermediate Similarity NPC174447
0.7458 Intermediate Similarity NPC122521
0.7458 Intermediate Similarity NPC243532
0.7455 Intermediate Similarity NPC309606
0.7455 Intermediate Similarity NPC39633
0.7455 Intermediate Similarity NPC139545
0.7447 Intermediate Similarity NPC73245
0.7414 Intermediate Similarity NPC329819
0.74 Intermediate Similarity NPC74845
0.7333 Intermediate Similarity NPC201939
0.7333 Intermediate Similarity NPC40082
0.7308 Intermediate Similarity NPC42304
0.7292 Intermediate Similarity NPC214610
0.7292 Intermediate Similarity NPC183424
0.7292 Intermediate Similarity NPC294085
0.7292 Intermediate Similarity NPC118968
0.7273 Intermediate Similarity NPC129458
0.7234 Intermediate Similarity NPC158179
0.7193 Intermediate Similarity NPC28779
0.7193 Intermediate Similarity NPC10316
0.7193 Intermediate Similarity NPC128061
0.7193 Intermediate Similarity NPC223677
0.7193 Intermediate Similarity NPC200845
0.7193 Intermediate Similarity NPC228473
0.717 Intermediate Similarity NPC91495
0.7143 Intermediate Similarity NPC225066
0.7143 Intermediate Similarity NPC10081
0.7143 Intermediate Similarity NPC71761
0.7119 Intermediate Similarity NPC34416
0.7115 Intermediate Similarity NPC30195
0.7115 Intermediate Similarity NPC12438
0.7115 Intermediate Similarity NPC117572
0.7097 Intermediate Similarity NPC68343
0.7097 Intermediate Similarity NPC328089
0.7091 Intermediate Similarity NPC100096
0.7083 Intermediate Similarity NPC268826
0.7049 Intermediate Similarity NPC125312
0.7049 Intermediate Similarity NPC477829
0.7049 Intermediate Similarity NPC174560
0.7021 Intermediate Similarity NPC155263
0.6984 Remote Similarity NPC326268
0.6984 Remote Similarity NPC245947
0.6984 Remote Similarity NPC318420
0.6984 Remote Similarity NPC255863
0.6984 Remote Similarity NPC136164
0.6981 Remote Similarity NPC328497
0.6981 Remote Similarity NPC324004
0.6981 Remote Similarity NPC21844
0.6964 Remote Similarity NPC303765
0.6923 Remote Similarity NPC55023
0.6897 Remote Similarity NPC477984
0.6897 Remote Similarity NPC52264
0.6897 Remote Similarity NPC474672
0.6852 Remote Similarity NPC477878
0.6852 Remote Similarity NPC106872
0.6852 Remote Similarity NPC324793
0.6833 Remote Similarity NPC469373
0.6825 Remote Similarity NPC234767
0.6809 Remote Similarity NPC156630
0.68 Remote Similarity NPC28598
0.68 Remote Similarity NPC161097
0.68 Remote Similarity NPC12156
0.6792 Remote Similarity NPC314679
0.6786 Remote Similarity NPC48162
0.678 Remote Similarity NPC325977
0.6774 Remote Similarity NPC321838
0.6774 Remote Similarity NPC320305
0.6774 Remote Similarity NPC328776
0.6769 Remote Similarity NPC99619
0.6769 Remote Similarity NPC271921
0.6769 Remote Similarity NPC330426
0.6769 Remote Similarity NPC148192
0.6769 Remote Similarity NPC26500
0.6769 Remote Similarity NPC22101
0.6769 Remote Similarity NPC104537
0.6769 Remote Similarity NPC127091
0.6735 Remote Similarity NPC201622
0.6735 Remote Similarity NPC22903
0.6735 Remote Similarity NPC305660
0.6735 Remote Similarity NPC54980
0.6724 Remote Similarity NPC137538
0.6667 Remote Similarity NPC310746
0.6667 Remote Similarity NPC324981
0.6667 Remote Similarity NPC29697
0.6667 Remote Similarity NPC134782
0.6667 Remote Similarity NPC473559
0.6667 Remote Similarity NPC48218
0.6667 Remote Similarity NPC476614
0.6667 Remote Similarity NPC141481
0.6667 Remote Similarity NPC473705
0.6615 Remote Similarity NPC308294
0.6615 Remote Similarity NPC142423
0.6613 Remote Similarity NPC45097
0.6613 Remote Similarity NPC229252
0.6613 Remote Similarity NPC143857
0.6607 Remote Similarity NPC474391
0.6607 Remote Similarity NPC90904
0.66 Remote Similarity NPC31551
0.66 Remote Similarity NPC219536
0.6571 Remote Similarity NPC81052
0.6567 Remote Similarity NPC317583
0.6567 Remote Similarity NPC143396
0.6562 Remote Similarity NPC53642
0.6562 Remote Similarity NPC470325
0.6545 Remote Similarity NPC200618
0.6545 Remote Similarity NPC131770
0.6538 Remote Similarity NPC236579
0.6538 Remote Similarity NPC203531
0.6515 Remote Similarity NPC60120
0.6515 Remote Similarity NPC473829
0.6515 Remote Similarity NPC475443
0.6508 Remote Similarity NPC271282
0.6508 Remote Similarity NPC325929
0.6508 Remote Similarity NPC475984
0.6508 Remote Similarity NPC66460
0.6471 Remote Similarity NPC42526
0.6471 Remote Similarity NPC476660
0.6471 Remote Similarity NPC165533
0.6471 Remote Similarity NPC256163
0.6471 Remote Similarity NPC250028
0.6471 Remote Similarity NPC40597
0.6471 Remote Similarity NPC149299
0.6452 Remote Similarity NPC329550
0.6441 Remote Similarity NPC322461
0.6429 Remote Similarity NPC207815
0.6429 Remote Similarity NPC26253

  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 NPC470410 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
0.8571 High Similarity NPD622 Approved
0.8462 Intermediate Similarity NPD3172 Approved
0.8302 Intermediate Similarity NPD4266 Approved
0.8302 Intermediate Similarity NPD3194 Approved
0.8302 Intermediate Similarity NPD3195 Phase 2
0.8302 Intermediate Similarity NPD3196 Approved
0.7736 Intermediate Similarity NPD29 Approved
0.7736 Intermediate Similarity NPD28 Approved
0.7708 Intermediate Similarity NPD2270 Approved
0.7692 Intermediate Similarity NPD3173 Approved
0.766 Intermediate Similarity NPD633 Phase 3
0.766 Intermediate Similarity NPD9448 Phase 2
0.7292 Intermediate Similarity NPD9655 Approved
0.7255 Intermediate Similarity NPD3199 Clinical (unspecified phase)
0.7115 Intermediate Similarity NPD4222 Approved
0.7115 Intermediate Similarity NPD3174 Discontinued
0.7097 Intermediate Similarity NPD3197 Phase 1
0.7083 Intermediate Similarity NPD3206 Approved
0.6792 Remote Similarity NPD39 Approved
0.6792 Remote Similarity NPD634 Phase 3
0.6415 Remote Similarity NPD5326 Phase 3
0.6406 Remote Similarity NPD2664 Clinical (unspecified phase)
0.6379 Remote Similarity NPD3186 Phase 1
0.6349 Remote Similarity NPD4246 Clinical (unspecified phase)
0.6296 Remote Similarity NPD2699 Approved
0.6226 Remote Similarity NPD387 Clinical (unspecified phase)
0.6182 Remote Similarity NPD9430 Approved
0.6182 Remote Similarity NPD9431 Approved
0.6167 Remote Similarity NPD3730 Approved
0.6167 Remote Similarity NPD3729 Clinical (unspecified phase)
0.6167 Remote Similarity NPD3728 Approved
0.6154 Remote Similarity NPD9635 Discontinued
0.6119 Remote Similarity NPD7331 Phase 2
0.6066 Remote Similarity NPD4627 Clinical (unspecified phase)
0.5965 Remote Similarity NPD5343 Approved
0.5962 Remote Similarity NPD77 Approved
0.5962 Remote Similarity NPD9450 Approved
0.5946 Remote Similarity NPD4756 Discovery
0.5902 Remote Similarity NPD615 Clinical (unspecified phase)
0.5867 Remote Similarity NPD3732 Approved
0.5797 Remote Similarity NPD4247 Clinical (unspecified phase)
0.5769 Remote Similarity NPD9513 Phase 1
0.5735 Remote Similarity NPD7341 Phase 2
0.5714 Remote Similarity NPD5368 Approved
0.5696 Remote Similarity NPD5332 Approved
0.5696 Remote Similarity NPD5331 Approved
0.5692 Remote Similarity NPD3198 Approved
0.569 Remote Similarity NPD6125 Clinical (unspecified phase)
0.569 Remote Similarity NPD2266 Phase 2
0.5667 Remote Similarity NPD9638 Phase 2
0.5658 Remote Similarity NPD5784 Clinical (unspecified phase)
0.5652 Remote Similarity NPD3704 Approved
0.5641 Remote Similarity NPD5369 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