Structure

Physi-Chem Properties

Molecular Weight:  246.13
Volume:  275.912
LogP:  3.189
LogD:  2.233
LogS:  -2.831
# Rotatable Bonds:  6
TPSA:  57.53
# H-Bond Aceptor:  3
# H-Bond Donor:  2
# Rings:  0
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.429
Synthetic Accessibility Score:  4.202
Fsp3:  0.467
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.902
MDCK Permeability:  2.6397288820589893e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.002
Human Intestinal Absorption (HIA):  0.651
20% Bioavailability (F20%):  0.003
30% Bioavailability (F30%):  0.276

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.044
Plasma Protein Binding (PPB):  99.2126693725586%
Volume Distribution (VD):  0.462
Pgp-substrate:  1.758994698524475%

ADMET: Metabolism

CYP1A2-inhibitor:  0.015
CYP1A2-substrate:  0.095
CYP2C19-inhibitor:  0.332
CYP2C19-substrate:  0.139
CYP2C9-inhibitor:  0.276
CYP2C9-substrate:  0.988
CYP2D6-inhibitor:  0.002
CYP2D6-substrate:  0.057
CYP3A4-inhibitor:  0.08
CYP3A4-substrate:  0.023

ADMET: Excretion

Clearance (CL):  3.753
Half-life (T1/2):  0.91

ADMET: Toxicity

hERG Blockers:  0.009
Human Hepatotoxicity (H-HT):  0.963
Drug-inuced Liver Injury (DILI):  0.981
AMES Toxicity:  0.729
Rat Oral Acute Toxicity:  0.968
Maximum Recommended Daily Dose:  0.947
Skin Sensitization:  0.949
Carcinogencity:  0.417
Eye Corrosion:  0.341
Eye Irritation:  0.794
Respiratory Toxicity:  0.961

Download Data

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

  Natural Product: NPC470411

Natural Product ID:  NPC470411
Common Name*:   Phomallenic Acid A
IUPAC Name:   13-hydroxypentadeca-6,7-dien-9,11-diynoic acid
Synonyms:  
Standard InCHIKey:  YZCDHRPWTDTXRF-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C15H18O3/c1-2-14(16)12-10-8-6-4-3-5-7-9-11-13-15(17)18/h4-5,14,16H,2,7,9,11,13H2,1H3,(H,17,18)
SMILES:  CCC(C#CC#CC=C=CCCCCC(=O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2028080
PubChem CID:   11680354
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 = 0.63 ug ml-1 PMID[502720]
NPT2 Others Unspecified IC50 = 22.0 ug.mL-1 PMID[502720]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC = 250.0 ug.mL-1 PMID[502720]
NPT175 Organism Enterococcus faecalis Enterococcus faecalis MIC > 250.0 ug.mL-1 PMID[502720]
NPT1531 Organism Enterococcus faecium Enterococcus faecium MIC > 250.0 ug.mL-1 PMID[502720]
NPT19 Organism Escherichia coli Escherichia coli MIC > 250.0 ug.mL-1 PMID[502720]
NPT19 Organism Escherichia coli Escherichia coli MIC = 31.3 ug.mL-1 PMID[502720]

☑ 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 NPC470411 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
0.8077 Intermediate Similarity NPC28205
0.8077 Intermediate Similarity NPC470410
0.8077 Intermediate Similarity NPC470412
0.7736 Intermediate Similarity NPC284212
0.7692 Intermediate Similarity NPC304162
0.7667 Intermediate Similarity NPC226592
0.7667 Intermediate Similarity NPC470320
0.7593 Intermediate Similarity NPC18357
0.7547 Intermediate Similarity NPC473487
0.75 Intermediate Similarity NPC274290
0.75 Intermediate Similarity NPC473863
0.7458 Intermediate Similarity NPC243532
0.7447 Intermediate Similarity NPC73245
0.7368 Intermediate Similarity NPC187777
0.7368 Intermediate Similarity NPC179764
0.7358 Intermediate Similarity NPC149821
0.7358 Intermediate Similarity NPC5413
0.7333 Intermediate Similarity NPC201939
0.7333 Intermediate Similarity NPC477829
0.7321 Intermediate Similarity NPC137538
0.7308 Intermediate Similarity NPC42304
0.7273 Intermediate Similarity NPC161366
0.7273 Intermediate Similarity NPC473705
0.7241 Intermediate Similarity NPC323436
0.7193 Intermediate Similarity NPC54766
0.7193 Intermediate Similarity NPC52264
0.717 Intermediate Similarity NPC207292
0.717 Intermediate Similarity NPC180534
0.7167 Intermediate Similarity NPC327112
0.7091 Intermediate Similarity NPC100096
0.7069 Intermediate Similarity NPC327388
0.7049 Intermediate Similarity NPC113293
0.7049 Intermediate Similarity NPC321838
0.7 Intermediate Similarity NPC163746
0.7 Intermediate Similarity NPC103286
0.6984 Remote Similarity NPC323045
0.6984 Remote Similarity NPC245947
0.6984 Remote Similarity NPC317881
0.6984 Remote Similarity NPC136164
0.6984 Remote Similarity NPC255863
0.6981 Remote Similarity NPC328497
0.6981 Remote Similarity NPC324004
0.6964 Remote Similarity NPC92114
0.6964 Remote Similarity NPC281245
0.6964 Remote Similarity NPC129458
0.6949 Remote Similarity NPC323597
0.6949 Remote Similarity NPC225929
0.6949 Remote Similarity NPC323498
0.6949 Remote Similarity NPC211752
0.6935 Remote Similarity NPC29697
0.6885 Remote Similarity NPC328311
0.6885 Remote Similarity NPC81896
0.6885 Remote Similarity NPC321919
0.6885 Remote Similarity NPC235242
0.6875 Remote Similarity NPC158179
0.6863 Remote Similarity NPC71317
0.6863 Remote Similarity NPC129972
0.6863 Remote Similarity NPC301528
0.6852 Remote Similarity NPC106872
0.6852 Remote Similarity NPC91495
0.6852 Remote Similarity NPC131770
0.6852 Remote Similarity NPC216130
0.6852 Remote Similarity NPC200618
0.6842 Remote Similarity NPC36061
0.6842 Remote Similarity NPC139029
0.6842 Remote Similarity NPC284224
0.6842 Remote Similarity NPC321062
0.6842 Remote Similarity NPC1813
0.6842 Remote Similarity NPC294548
0.6842 Remote Similarity NPC70387
0.6842 Remote Similarity NPC10081
0.6842 Remote Similarity NPC225066
0.6833 Remote Similarity NPC267817
0.6825 Remote Similarity NPC68343
0.6825 Remote Similarity NPC328089
0.6809 Remote Similarity NPC317203
0.6792 Remote Similarity NPC117572
0.678 Remote Similarity NPC477201
0.6774 Remote Similarity NPC325929
0.6774 Remote Similarity NPC475984
0.6774 Remote Similarity NPC320305
0.6774 Remote Similarity NPC328776
0.6774 Remote Similarity NPC271282
0.6774 Remote Similarity NPC66460
0.6769 Remote Similarity NPC99619
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 NPC271921
0.6769 Remote Similarity NPC49863
0.6769 Remote Similarity NPC127091
0.6731 Remote Similarity NPC255837
0.6731 Remote Similarity NPC19305
0.6727 Remote Similarity NPC163345
0.6724 Remote Similarity NPC25417
0.6724 Remote Similarity NPC6095
0.6724 Remote Similarity NPC85813
0.6724 Remote Similarity NPC32467
0.6724 Remote Similarity NPC261831
0.6724 Remote Similarity NPC87564
0.6724 Remote Similarity NPC281972
0.6724 Remote Similarity NPC154245
0.6724 Remote Similarity NPC88966
0.6724 Remote Similarity NPC290563
0.6724 Remote Similarity NPC424
0.6721 Remote Similarity NPC329249
0.6721 Remote Similarity NPC318306
0.6721 Remote Similarity NPC322002
0.6719 Remote Similarity NPC323477
0.6719 Remote Similarity NPC318420
0.6719 Remote Similarity NPC320642
0.6719 Remote Similarity NPC326268
0.6667 Remote Similarity NPC470965
0.6667 Remote Similarity NPC472445
0.6667 Remote Similarity NPC477980
0.6667 Remote Similarity NPC303765
0.6667 Remote Similarity NPC324981
0.6667 Remote Similarity NPC473559
0.6667 Remote Similarity NPC48218
0.6667 Remote Similarity NPC141481
0.6615 Remote Similarity NPC328653
0.661 Remote Similarity NPC45626
0.6607 Remote Similarity NPC59051
0.6607 Remote Similarity NPC90904
0.6604 Remote Similarity NPC8219
0.6571 Remote Similarity NPC81052
0.6567 Remote Similarity NPC143396
0.6557 Remote Similarity NPC469373
0.6557 Remote Similarity NPC329819
0.6552 Remote Similarity NPC217188
0.6538 Remote Similarity NPC249801
0.6538 Remote Similarity NPC46248
0.6515 Remote Similarity NPC25298
0.6515 Remote Similarity NPC473829
0.6515 Remote Similarity NPC475443
0.65 Remote Similarity NPC325977
0.65 Remote Similarity NPC324224
0.65 Remote Similarity NPC472808
0.65 Remote Similarity NPC18951
0.6491 Remote Similarity NPC48162
0.6481 Remote Similarity NPC30195
0.6481 Remote Similarity NPC172042
0.6481 Remote Similarity NPC12438
0.6471 Remote Similarity NPC42526
0.6471 Remote Similarity NPC476660
0.6462 Remote Similarity NPC476657
0.6462 Remote Similarity NPC476655
0.6462 Remote Similarity NPC476654
0.6452 Remote Similarity NPC106851
0.6452 Remote Similarity NPC222852
0.6452 Remote Similarity NPC329550
0.6452 Remote Similarity NPC274927
0.6441 Remote Similarity NPC110732
0.6441 Remote Similarity NPC256209
0.6441 Remote Similarity NPC300121
0.6441 Remote Similarity NPC322461
0.6441 Remote Similarity NPC49059
0.6429 Remote Similarity NPC302310
0.6393 Remote Similarity NPC44542
0.6393 Remote Similarity NPC212730
0.6393 Remote Similarity NPC265551
0.6383 Remote Similarity NPC175342
0.6379 Remote Similarity NPC216407
0.6377 Remote Similarity NPC474590
0.6377 Remote Similarity NPC320119
0.6377 Remote Similarity NPC477983
0.6377 Remote Similarity NPC477981
0.6364 Remote Similarity NPC476656
0.6364 Remote Similarity NPC476659
0.6351 Remote Similarity NPC200446
0.6349 Remote Similarity NPC174447
0.6349 Remote Similarity NPC251042
0.6349 Remote Similarity NPC122521
0.6346 Remote Similarity NPC474361
0.6333 Remote Similarity NPC474513
0.6333 Remote Similarity NPC152668
0.6333 Remote Similarity NPC470963
0.6333 Remote Similarity NPC223677
0.6333 Remote Similarity NPC28779
0.6333 Remote Similarity NPC10316
0.6333 Remote Similarity NPC146551
0.6333 Remote Similarity NPC128061
0.6333 Remote Similarity NPC474672
0.6333 Remote Similarity NPC200845
0.6327 Remote Similarity NPC154642
0.6327 Remote Similarity NPC80396
0.6324 Remote Similarity NPC473772
0.6324 Remote Similarity NPC236208
0.6324 Remote Similarity NPC130618
0.6324 Remote Similarity NPC317583
0.6316 Remote Similarity NPC225974
0.6316 Remote Similarity NPC224227
0.6301 Remote Similarity NPC469495
0.6296 Remote Similarity NPC469781
0.6286 Remote Similarity NPC326024
0.6286 Remote Similarity NPC325627
0.6275 Remote Similarity NPC301585
0.6275 Remote Similarity NPC201844

  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 NPC470411 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
0.7358 Intermediate Similarity NPD3173 Approved
0.717 Intermediate Similarity NPD622 Approved
0.7167 Intermediate Similarity NPD4246 Clinical (unspecified phase)
0.7097 Intermediate Similarity NPD3197 Phase 1
0.6842 Remote Similarity NPD3172 Approved
0.6792 Remote Similarity NPD3174 Discontinued
0.6792 Remote Similarity NPD4222 Approved
0.6769 Remote Similarity NPD4247 Clinical (unspecified phase)
0.6724 Remote Similarity NPD3194 Approved
0.6724 Remote Similarity NPD3195 Phase 2
0.6724 Remote Similarity NPD4266 Approved
0.6724 Remote Similarity NPD3196 Approved
0.6481 Remote Similarity NPD39 Approved
0.629 Remote Similarity NPD6109 Phase 1
0.6275 Remote Similarity NPD9448 Phase 2
0.6275 Remote Similarity NPD633 Phase 3
0.625 Remote Similarity NPD5343 Approved
0.6207 Remote Similarity NPD28 Approved
0.6207 Remote Similarity NPD29 Approved
0.6167 Remote Similarity NPD3728 Approved
0.6167 Remote Similarity NPD3730 Approved
0.6167 Remote Similarity NPD3729 Clinical (unspecified phase)
0.6154 Remote Similarity NPD9635 Discontinued
0.6111 Remote Similarity NPD5326 Phase 3
0.6066 Remote Similarity NPD4627 Clinical (unspecified phase)
0.6038 Remote Similarity NPD2270 Approved
0.6 Remote Similarity NPD2699 Approved
0.5965 Remote Similarity NPD2266 Phase 2
0.5962 Remote Similarity NPD9655 Approved
0.5897 Remote Similarity NPD5331 Approved
0.5897 Remote Similarity NPD5332 Approved
0.5867 Remote Similarity NPD5784 Clinical (unspecified phase)
0.5714 Remote Similarity NPD6097 Approved
0.5714 Remote Similarity NPD5368 Approved
0.5714 Remote Similarity NPD4252 Approved
0.5714 Remote Similarity NPD6096 Approved
0.5714 Remote Similarity NPD3199 Clinical (unspecified phase)
0.5692 Remote Similarity NPD3198 Approved
0.569 Remote Similarity NPD6125 Clinical (unspecified phase)
0.566 Remote Similarity NPD77 Approved
0.566 Remote Similarity NPD9450 Approved
0.5658 Remote Similarity NPD4268 Approved
0.5658 Remote Similarity NPD4271 Approved
0.5641 Remote Similarity NPD5369 Approved
0.5614 Remote Similarity NPD634 Phase 3
0.56 Remote Similarity NPD8857 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