Structure

Physi-Chem Properties

Molecular Weight:  274.19
Volume:  321.646
LogP:  5.415
LogD:  2.811
LogS:  -4.71
# Rotatable Bonds:  10
TPSA:  37.3
# H-Bond Aceptor:  2
# H-Bond Donor:  1
# Rings:  0
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.468
Synthetic Accessibility Score:  2.839
Fsp3:  0.611
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:  -4.723
MDCK Permeability:  4.5449774916050956e-05
Pgp-inhibitor:  0.003
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.013
20% Bioavailability (F20%):  0.367
30% Bioavailability (F30%):  0.99

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.003
Plasma Protein Binding (PPB):  101.37803649902344%
Volume Distribution (VD):  0.44
Pgp-substrate:  0.6217049956321716%

ADMET: Metabolism

CYP1A2-inhibitor:  0.6
CYP1A2-substrate:  0.211
CYP2C19-inhibitor:  0.888
CYP2C19-substrate:  0.55
CYP2C9-inhibitor:  0.837
CYP2C9-substrate:  0.998
CYP2D6-inhibitor:  0.148
CYP2D6-substrate:  0.826
CYP3A4-inhibitor:  0.583
CYP3A4-substrate:  0.034

ADMET: Excretion

Clearance (CL):  1.824
Half-life (T1/2):  0.708

ADMET: Toxicity

hERG Blockers:  0.01
Human Hepatotoxicity (H-HT):  0.736
Drug-inuced Liver Injury (DILI):  0.974
AMES Toxicity:  0.504
Rat Oral Acute Toxicity:  0.032
Maximum Recommended Daily Dose:  0.024
Skin Sensitization:  0.953
Carcinogencity:  0.385
Eye Corrosion:  0.976
Eye Irritation:  0.974
Respiratory Toxicity:  0.873

Download Data

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

  Natural Product: NPC187777

Natural Product ID:  NPC187777
Common Name*:   Exocarpic Acid
IUPAC Name:   (E)-octadec-13-en-9,11-diynoic acid
Synonyms:   Exocarpic Acid
Standard InCHIKey:  ACHMRCSARDWYGC-AATRIKPKSA-N
Standard InCHI:  InChI=1S/C18H26O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18(19)20/h5-6H,2-4,11-17H2,1H3,(H,19,20)/b6-5+
SMILES:  CCCC/C=C/C#CC#CCCCCCCCC(=O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2204412
PubChem CID:   5312684
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
NPO3779 Sassafras tzumu Species Lauraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO3158 Linum album Species Linaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO3158 Linum album Species Linaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3779 Sassafras tzumu Species Lauraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7353 Euphorbia paralias Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3779 Sassafras tzumu Species Lauraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO3158 Linum album Species Linaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO12793 Clibadium glomeratum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3779 Sassafras tzumu Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4678 Galanthus caucasicus Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25591 Vexibia alopecuroides n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO7353 Euphorbia paralias Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6282 Pestalotia ramulosa Species Amphisphaeriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3158 Linum album Species Linaceae 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
NPT790 Organism Mycobacterium tuberculosis H37Rv Mycobacterium tuberculosis H37Rv MIC = 87.0 ug.mL-1 PMID[572860]
NPT790 Organism Mycobacterium tuberculosis H37Rv Mycobacterium tuberculosis H37Rv MIC = 20.0 ug.mL-1 PMID[572860]
NPT115 Organism Mycobacterium tuberculosis H37Ra Mycobacterium tuberculosis H37Ra MIC = 20.0 ug.mL-1 PMID[572860]

☑ 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 NPC187777 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 NPC179764
0.9808 High Similarity NPC274290
0.9808 High Similarity NPC54766
0.9808 High Similarity NPC473863
0.9444 High Similarity NPC225929
0.9423 High Similarity NPC139029
0.9423 High Similarity NPC36061
0.9423 High Similarity NPC1813
0.9423 High Similarity NPC294548
0.9245 High Similarity NPC85813
0.9245 High Similarity NPC154245
0.9245 High Similarity NPC424
0.9245 High Similarity NPC290563
0.9245 High Similarity NPC87564
0.9245 High Similarity NPC32467
0.9245 High Similarity NPC281972
0.9245 High Similarity NPC88966
0.9245 High Similarity NPC25417
0.9245 High Similarity NPC261831
0.9245 High Similarity NPC6095
0.9231 High Similarity NPC281245
0.9231 High Similarity NPC18357
0.9057 High Similarity NPC70387
0.9057 High Similarity NPC321062
0.9038 High Similarity NPC28205
0.9038 High Similarity NPC470410
0.9038 High Similarity NPC470412
0.9038 High Similarity NPC284212
0.8947 High Similarity NPC235242
0.8929 High Similarity NPC267817
0.8909 High Similarity NPC18951
0.8909 High Similarity NPC477201
0.8868 High Similarity NPC92114
0.8846 High Similarity NPC224227
0.8679 High Similarity NPC262968
0.8654 High Similarity NPC5413
0.8654 High Similarity NPC149821
0.8519 High Similarity NPC161366
0.85 High Similarity NPC470320
0.85 High Similarity NPC226592
0.8491 Intermediate Similarity NPC59051
0.8462 Intermediate Similarity NPC180534
0.8462 Intermediate Similarity NPC207292
0.8448 Intermediate Similarity NPC106851
0.8448 Intermediate Similarity NPC274927
0.8393 Intermediate Similarity NPC45626
0.8364 Intermediate Similarity NPC39633
0.8364 Intermediate Similarity NPC309606
0.8364 Intermediate Similarity NPC139545
0.8305 Intermediate Similarity NPC174447
0.8305 Intermediate Similarity NPC122521
0.8305 Intermediate Similarity NPC251042
0.8305 Intermediate Similarity NPC243532
0.8276 Intermediate Similarity NPC329819
0.8269 Intermediate Similarity NPC42304
0.8182 Intermediate Similarity NPC129458
0.8167 Intermediate Similarity NPC201939
0.8167 Intermediate Similarity NPC40082
0.8113 Intermediate Similarity NPC91495
0.8077 Intermediate Similarity NPC117572
0.807 Intermediate Similarity NPC200845
0.807 Intermediate Similarity NPC28779
0.807 Intermediate Similarity NPC223677
0.807 Intermediate Similarity NPC10316
0.807 Intermediate Similarity NPC228473
0.807 Intermediate Similarity NPC128061
0.8036 Intermediate Similarity NPC71761
0.8036 Intermediate Similarity NPC225066
0.8036 Intermediate Similarity NPC10081
0.7966 Intermediate Similarity NPC34416
0.7903 Intermediate Similarity NPC68343
0.7903 Intermediate Similarity NPC328089
0.7895 Intermediate Similarity NPC87394
0.7869 Intermediate Similarity NPC125312
0.7869 Intermediate Similarity NPC174560
0.7869 Intermediate Similarity NPC477829
0.7857 Intermediate Similarity NPC303765
0.7778 Intermediate Similarity NPC216130
0.7778 Intermediate Similarity NPC326268
0.7778 Intermediate Similarity NPC255863
0.7778 Intermediate Similarity NPC136164
0.7778 Intermediate Similarity NPC318420
0.7778 Intermediate Similarity NPC245947
0.7759 Intermediate Similarity NPC477984
0.7759 Intermediate Similarity NPC52264
0.7759 Intermediate Similarity NPC474672
0.7692 Intermediate Similarity NPC19305
0.7692 Intermediate Similarity NPC255837
0.7679 Intermediate Similarity NPC48162
0.7667 Intermediate Similarity NPC469373
0.7627 Intermediate Similarity NPC325977
0.7586 Intermediate Similarity NPC137538
0.7581 Intermediate Similarity NPC320305
0.7581 Intermediate Similarity NPC321838
0.7581 Intermediate Similarity NPC328776
0.7547 Intermediate Similarity NPC8219
0.7538 Intermediate Similarity NPC22101
0.7538 Intermediate Similarity NPC330426
0.7538 Intermediate Similarity NPC127091
0.7538 Intermediate Similarity NPC26500
0.7538 Intermediate Similarity NPC99619
0.7538 Intermediate Similarity NPC148192
0.7538 Intermediate Similarity NPC104537
0.7538 Intermediate Similarity NPC271921
0.746 Intermediate Similarity NPC29697
0.7424 Intermediate Similarity NPC473559
0.7424 Intermediate Similarity NPC141481
0.7424 Intermediate Similarity NPC48218
0.7424 Intermediate Similarity NPC324981
0.7424 Intermediate Similarity NPC476614
0.7419 Intermediate Similarity NPC143857
0.7419 Intermediate Similarity NPC229252
0.7368 Intermediate Similarity NPC470411
0.7358 Intermediate Similarity NPC270796
0.7344 Intermediate Similarity NPC234767
0.7321 Intermediate Similarity NPC207815
0.7313 Intermediate Similarity NPC143396
0.7313 Intermediate Similarity NPC317583
0.7308 Intermediate Similarity NPC103286
0.7308 Intermediate Similarity NPC163746
0.7302 Intermediate Similarity NPC271282
0.7302 Intermediate Similarity NPC66460
0.7302 Intermediate Similarity NPC325929
0.7302 Intermediate Similarity NPC475984
0.7288 Intermediate Similarity NPC322461
0.7273 Intermediate Similarity NPC473829
0.7273 Intermediate Similarity NPC60120
0.7273 Intermediate Similarity NPC475443
0.7258 Intermediate Similarity NPC329550
0.7206 Intermediate Similarity NPC476660
0.7206 Intermediate Similarity NPC42526
0.7193 Intermediate Similarity NPC474391
0.7188 Intermediate Similarity NPC477707
0.7188 Intermediate Similarity NPC54925
0.7188 Intermediate Similarity NPC470965
0.717 Intermediate Similarity NPC129972
0.717 Intermediate Similarity NPC71317
0.717 Intermediate Similarity NPC301528
0.7164 Intermediate Similarity NPC53302
0.7143 Intermediate Similarity NPC328311
0.7143 Intermediate Similarity NPC327112
0.7121 Intermediate Similarity NPC142423
0.7121 Intermediate Similarity NPC308294
0.7119 Intermediate Similarity NPC284224
0.7069 Intermediate Similarity NPC129263
0.7069 Intermediate Similarity NPC477458
0.7059 Intermediate Similarity NPC473772
0.7049 Intermediate Similarity NPC327388
0.7027 Intermediate Similarity NPC200446
0.7018 Intermediate Similarity NPC304162
0.7018 Intermediate Similarity NPC163345
0.7 Intermediate Similarity NPC256209
0.7 Intermediate Similarity NPC49059
0.6986 Remote Similarity NPC469495
0.6984 Remote Similarity NPC474267
0.6981 Remote Similarity NPC307783
0.6981 Remote Similarity NPC171736
0.6981 Remote Similarity NPC196924
0.6981 Remote Similarity NPC149184
0.6981 Remote Similarity NPC209970
0.6981 Remote Similarity NPC216630
0.6935 Remote Similarity NPC323436
0.6935 Remote Similarity NPC323597
0.6935 Remote Similarity NPC323498
0.6935 Remote Similarity NPC211752
0.6923 Remote Similarity NPC477830
0.6923 Remote Similarity NPC301696
0.6923 Remote Similarity NPC14227
0.6923 Remote Similarity NPC261080
0.6923 Remote Similarity NPC279026
0.6923 Remote Similarity NPC113928
0.6923 Remote Similarity NPC201844
0.6923 Remote Similarity NPC301585
0.6923 Remote Similarity NPC154186
0.6909 Remote Similarity NPC108195
0.6901 Remote Similarity NPC3753
0.6901 Remote Similarity NPC283908
0.6901 Remote Similarity NPC476046
0.6901 Remote Similarity NPC241854
0.6901 Remote Similarity NPC227396
0.6901 Remote Similarity NPC103958
0.6901 Remote Similarity NPC251970
0.6901 Remote Similarity NPC474321
0.6901 Remote Similarity NPC183503
0.6901 Remote Similarity NPC55527
0.6901 Remote Similarity NPC161923
0.6901 Remote Similarity NPC237591
0.6892 Remote Similarity NPC209995
0.6875 Remote Similarity NPC299730
0.6857 Remote Similarity NPC318814
0.6857 Remote Similarity NPC186531
0.6857 Remote Similarity NPC288667
0.6857 Remote Similarity NPC477981
0.6857 Remote Similarity NPC320119
0.6857 Remote Similarity NPC320669
0.6857 Remote Similarity NPC477983
0.6857 Remote Similarity NPC160817
0.6852 Remote Similarity NPC67462
0.6833 Remote Similarity NPC34577
0.6833 Remote Similarity NPC26102

  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 NPC187777 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
0.9423 High Similarity NPD3172 Approved
0.9245 High Similarity NPD3194 Approved
0.9245 High Similarity NPD3195 Phase 2
0.9245 High Similarity NPD4266 Approved
0.9245 High Similarity NPD3196 Approved
0.8679 High Similarity NPD29 Approved
0.8679 High Similarity NPD28 Approved
0.8654 High Similarity NPD3173 Approved
0.8462 Intermediate Similarity NPD622 Approved
0.8077 Intermediate Similarity NPD4222 Approved
0.8077 Intermediate Similarity NPD3174 Discontinued
0.7903 Intermediate Similarity NPD3197 Phase 1
0.7736 Intermediate Similarity NPD39 Approved
0.7358 Intermediate Similarity NPD5326 Phase 3
0.7143 Intermediate Similarity NPD4246 Clinical (unspecified phase)
0.6981 Remote Similarity NPD2270 Approved
0.6923 Remote Similarity NPD633 Phase 3
0.6923 Remote Similarity NPD9448 Phase 2
0.6842 Remote Similarity NPD5343 Approved
0.6667 Remote Similarity NPD2664 Clinical (unspecified phase)
0.6618 Remote Similarity NPD7331 Phase 2
0.6607 Remote Similarity NPD3199 Clinical (unspecified phase)
0.6604 Remote Similarity NPD9655 Approved
0.6533 Remote Similarity NPD3732 Approved
0.6522 Remote Similarity NPD4247 Clinical (unspecified phase)
0.6415 Remote Similarity NPD3206 Approved
0.64 Remote Similarity NPD4756 Discovery
0.6364 Remote Similarity NPD5368 Approved
0.6349 Remote Similarity NPD4627 Clinical (unspecified phase)
0.6329 Remote Similarity NPD5332 Approved
0.6329 Remote Similarity NPD5331 Approved
0.6316 Remote Similarity NPD6096 Approved
0.6316 Remote Similarity NPD6097 Approved
0.6316 Remote Similarity NPD5784 Clinical (unspecified phase)
0.6308 Remote Similarity NPD6109 Phase 1
0.6282 Remote Similarity NPD5369 Approved
0.6207 Remote Similarity NPD634 Phase 3
0.6203 Remote Similarity NPD6435 Approved
0.6203 Remote Similarity NPD4269 Approved
0.6203 Remote Similarity NPD4270 Approved
0.6154 Remote Similarity NPD4252 Approved
0.6143 Remote Similarity NPD6108 Clinical (unspecified phase)
0.6133 Remote Similarity NPD8039 Approved
0.6125 Remote Similarity NPD5362 Discontinued
0.6125 Remote Similarity NPD7154 Phase 3
0.6104 Remote Similarity NPD4268 Approved
0.6104 Remote Similarity NPD4271 Approved
0.6 Remote Similarity NPD7341 Phase 2
0.5976 Remote Similarity NPD5363 Approved
0.5949 Remote Similarity NPD4822 Approved
0.5949 Remote Similarity NPD5790 Clinical (unspecified phase)
0.5949 Remote Similarity NPD4821 Approved
0.5949 Remote Similarity NPD4820 Approved
0.5949 Remote Similarity NPD4819 Approved
0.5915 Remote Similarity NPD3704 Approved
0.5904 Remote Similarity NPD5786 Approved
0.5904 Remote Similarity NPD4519 Discontinued
0.5904 Remote Similarity NPD4623 Approved
0.5902 Remote Similarity NPD4220 Pre-registration
0.5875 Remote Similarity NPD857 Phase 3
0.5873 Remote Similarity NPD3186 Phase 1
0.5783 Remote Similarity NPD6082 Clinical (unspecified phase)
0.5765 Remote Similarity NPD4518 Approved
0.5763 Remote Similarity NPD2699 Approved
0.5714 Remote Similarity NPD6927 Phase 3
0.5714 Remote Similarity NPD4693 Phase 3
0.5714 Remote Similarity NPD4690 Approved
0.5714 Remote Similarity NPD4688 Approved
0.5714 Remote Similarity NPD4689 Approved
0.5714 Remote Similarity NPD4138 Approved
0.5714 Remote Similarity NPD5205 Approved
0.5698 Remote Similarity NPD5346 Phase 2
0.5698 Remote Similarity NPD5764 Clinical (unspecified phase)
0.5698 Remote Similarity NPD5347 Phase 2
0.5698 Remote Similarity NPD6101 Approved
0.5692 Remote Similarity NPD3728 Approved
0.5692 Remote Similarity NPD3730 Approved
0.5692 Remote Similarity NPD3729 Clinical (unspecified phase)
0.569 Remote Similarity NPD387 Clinical (unspecified phase)
0.5679 Remote Similarity NPD226 Approved
0.5679 Remote Similarity NPD4790 Discontinued
0.5667 Remote Similarity NPD9430 Approved
0.5667 Remote Similarity NPD9431 Approved
0.5647 Remote Similarity NPD4793 Discontinued
0.5632 Remote Similarity NPD5785 Approved
0.5614 Remote Similarity NPD9635 Discontinued

  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