Structure

Physi-Chem Properties

Molecular Weight:  478.4
Volume:  552.051
LogP:  5.467
LogD:  4.464
LogS:  -3.106
# Rotatable Bonds:  17
TPSA:  80.92
# H-Bond Aceptor:  4
# H-Bond Donor:  4
# Rings:  0
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.135
Synthetic Accessibility Score:  3.983
Fsp3:  0.733
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
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:  -4.839
MDCK Permeability:  2.4689745259820484e-05
Pgp-inhibitor:  0.574
Pgp-substrate:  0.955
Human Intestinal Absorption (HIA):  0.914
20% Bioavailability (F20%):  0.707
30% Bioavailability (F30%):  0.06

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.346
Plasma Protein Binding (PPB):  93.17053985595703%
Volume Distribution (VD):  1.001
Pgp-substrate:  1.7087223529815674%

ADMET: Metabolism

CYP1A2-inhibitor:  0.03
CYP1A2-substrate:  0.137
CYP2C19-inhibitor:  0.058
CYP2C19-substrate:  0.061
CYP2C9-inhibitor:  0.084
CYP2C9-substrate:  0.956
CYP2D6-inhibitor:  0.262
CYP2D6-substrate:  0.233
CYP3A4-inhibitor:  0.049
CYP3A4-substrate:  0.12

ADMET: Excretion

Clearance (CL):  3.263
Half-life (T1/2):  0.275

ADMET: Toxicity

hERG Blockers:  0.004
Human Hepatotoxicity (H-HT):  0.045
Drug-inuced Liver Injury (DILI):  0.002
AMES Toxicity:  0.001
Rat Oral Acute Toxicity:  0.001
Maximum Recommended Daily Dose:  0.976
Skin Sensitization:  0.955
Carcinogencity:  0.003
Eye Corrosion:  0.005
Eye Irritation:  0.27
Respiratory Toxicity:  0.004

Download Data

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

  Natural Product: NPC281590

Natural Product ID:  NPC281590
Common Name*:   (3R,22R)-2,6,10,15,19,23-Hexamethyltetracosa-6,10,14,18-Tetraene-2,3,22,23-Tetraol
IUPAC Name:   (3R,6E,10E,14E,18E,22R)-2,6,10,15,19,23-hexamethyltetracosa-6,10,14,18-tetraene-2,3,22,23-tetrol
Synonyms:  
Standard InCHIKey:  NPWAQSYSDCQSKY-LYINBSFCSA-N
Standard InCHI:  InChI=1S/C30H54O4/c1-23(15-11-17-25(3)19-21-27(31)29(5,6)33)13-9-10-14-24(2)16-12-18-26(4)20-22-28(32)30(7,8)34/h13-14,17-18,27-28,31-34H,9-12,15-16,19-22H2,1-8H3/b23-13+,24-14+,25-17+,26-18+/t27-,28-/m1/s1
SMILES:  O[C@@H](C(O)(C)C)CC/C(=C/CC/C(=C/CC/C=C(/CC/C=C(/CC[C@H](C(O)(C)C)O)C)C)/C)/C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL429678
PubChem CID:   11465741
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001553] Triterpenoids

*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
NPO9975 Ekebergia capensis Species Meliaceae Eukaryota n.a. n.a. n.a. PMID[18220356]
NPO33325 silphium laciniatum Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[26287548]
NPO9975 Ekebergia capensis Species Meliaceae 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
NPT397 Cell Line NCI-H460 Homo sapiens IC50 = 7000.0 nM PMID[555734]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum IC50 = 55000.0 nM PMID[555733]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum IC50 = 59000.0 nM PMID[555733]
NPT474 Organism Plasmodium berghei Plasmodium berghei Activity = 26.5 % PMID[555733]
NPT474 Organism Plasmodium berghei Plasmodium berghei Activity = 20.5 % PMID[555733]

☑ 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 NPC281590 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
0.9623 High Similarity NPC52012
0.8929 High Similarity NPC278202
0.8889 High Similarity NPC227135
0.8621 High Similarity NPC64971
0.8361 Intermediate Similarity NPC137163
0.8276 Intermediate Similarity NPC475931
0.8226 Intermediate Similarity NPC473357
0.8226 Intermediate Similarity NPC193029
0.8 Intermediate Similarity NPC475251
0.7969 Intermediate Similarity NPC472947
0.7969 Intermediate Similarity NPC16964
0.7966 Intermediate Similarity NPC122239
0.7963 Intermediate Similarity NPC329773
0.7857 Intermediate Similarity NPC474496
0.7833 Intermediate Similarity NPC469694
0.7818 Intermediate Similarity NPC473672
0.7818 Intermediate Similarity NPC474495
0.7797 Intermediate Similarity NPC226848
0.7797 Intermediate Similarity NPC181872
0.7656 Intermediate Similarity NPC73603
0.7636 Intermediate Similarity NPC474460
0.7619 Intermediate Similarity NPC308844
0.7619 Intermediate Similarity NPC471200
0.7586 Intermediate Similarity NPC329686
0.7547 Intermediate Similarity NPC165651
0.7547 Intermediate Similarity NPC24824
0.7547 Intermediate Similarity NPC210560
0.75 Intermediate Similarity NPC155025
0.75 Intermediate Similarity NPC250977
0.75 Intermediate Similarity NPC267027
0.7463 Intermediate Similarity NPC306085
0.7419 Intermediate Similarity NPC68679
0.7419 Intermediate Similarity NPC274704
0.7419 Intermediate Similarity NPC321867
0.7419 Intermediate Similarity NPC207007
0.7385 Intermediate Similarity NPC259299
0.7385 Intermediate Similarity NPC163290
0.7385 Intermediate Similarity NPC472253
0.7385 Intermediate Similarity NPC82337
0.7385 Intermediate Similarity NPC472255
0.7353 Intermediate Similarity NPC476709
0.7333 Intermediate Similarity NPC121034
0.7321 Intermediate Similarity NPC20934
0.7321 Intermediate Similarity NPC288381
0.7302 Intermediate Similarity NPC279200
0.7288 Intermediate Similarity NPC223604
0.7273 Intermediate Similarity NPC209327
0.7273 Intermediate Similarity NPC305698
0.7273 Intermediate Similarity NPC224532
0.7273 Intermediate Similarity NPC272961
0.7273 Intermediate Similarity NPC273508
0.7258 Intermediate Similarity NPC99487
0.7258 Intermediate Similarity NPC66020
0.7258 Intermediate Similarity NPC240506
0.7246 Intermediate Similarity NPC471525
0.7246 Intermediate Similarity NPC160540
0.7241 Intermediate Similarity NPC217188
0.7231 Intermediate Similarity NPC272125
0.7231 Intermediate Similarity NPC326310
0.7231 Intermediate Similarity NPC311736
0.7222 Intermediate Similarity NPC140501
0.7222 Intermediate Similarity NPC76976
0.7193 Intermediate Similarity NPC214584
0.7193 Intermediate Similarity NPC26906
0.7188 Intermediate Similarity NPC300593
0.7188 Intermediate Similarity NPC309300
0.7188 Intermediate Similarity NPC225415
0.7188 Intermediate Similarity NPC290367
0.7183 Intermediate Similarity NPC40049
0.7183 Intermediate Similarity NPC476703
0.7167 Intermediate Similarity NPC48891
0.7164 Intermediate Similarity NPC329989
0.7164 Intermediate Similarity NPC101622
0.7164 Intermediate Similarity NPC239373
0.7143 Intermediate Similarity NPC321838
0.7115 Intermediate Similarity NPC188596
0.7097 Intermediate Similarity NPC473866
0.7083 Intermediate Similarity NPC3852
0.7077 Intermediate Similarity NPC19569
0.7077 Intermediate Similarity NPC238352
0.7077 Intermediate Similarity NPC477009
0.7069 Intermediate Similarity NPC179169
0.7069 Intermediate Similarity NPC157781
0.7069 Intermediate Similarity NPC306195
0.7069 Intermediate Similarity NPC181255
0.7069 Intermediate Similarity NPC35756
0.7069 Intermediate Similarity NPC35519
0.7059 Intermediate Similarity NPC329904
0.7059 Intermediate Similarity NPC473361
0.7059 Intermediate Similarity NPC4299
0.7059 Intermediate Similarity NPC470041
0.7059 Intermediate Similarity NPC129630
0.7049 Intermediate Similarity NPC323436
0.7042 Intermediate Similarity NPC315261
0.7042 Intermediate Similarity NPC477925
0.7042 Intermediate Similarity NPC236228
0.7042 Intermediate Similarity NPC256720
0.7042 Intermediate Similarity NPC274079
0.7031 Intermediate Similarity NPC473508
0.7018 Intermediate Similarity NPC26960
0.7018 Intermediate Similarity NPC182102
0.7015 Intermediate Similarity NPC310210
0.7 Intermediate Similarity NPC251666
0.7 Intermediate Similarity NPC232247
0.6986 Remote Similarity NPC476701
0.6984 Remote Similarity NPC258788
0.6984 Remote Similarity NPC471081
0.6984 Remote Similarity NPC127824
0.6957 Remote Similarity NPC167706
0.6957 Remote Similarity NPC41886
0.6957 Remote Similarity NPC242992
0.6949 Remote Similarity NPC187361
0.6949 Remote Similarity NPC26102
0.6949 Remote Similarity NPC477724
0.6944 Remote Similarity NPC477924
0.6944 Remote Similarity NPC325946
0.6935 Remote Similarity NPC475830
0.6912 Remote Similarity NPC473893
0.6909 Remote Similarity NPC87439
0.6909 Remote Similarity NPC160628
0.6901 Remote Similarity NPC12696
0.6901 Remote Similarity NPC477923
0.6901 Remote Similarity NPC66566
0.6897 Remote Similarity NPC93639
0.6892 Remote Similarity NPC103634
0.6892 Remote Similarity NPC472948
0.6892 Remote Similarity NPC100697
0.6875 Remote Similarity NPC225342
0.6866 Remote Similarity NPC114651
0.6866 Remote Similarity NPC96962
0.6866 Remote Similarity NPC45782
0.6857 Remote Similarity NPC329763
0.6852 Remote Similarity NPC116934
0.6852 Remote Similarity NPC15162
0.6852 Remote Similarity NPC252978
0.6849 Remote Similarity NPC13823
0.6849 Remote Similarity NPC68119
0.6849 Remote Similarity NPC477089
0.6842 Remote Similarity NPC302310
0.6833 Remote Similarity NPC256209
0.6833 Remote Similarity NPC110732
0.6833 Remote Similarity NPC49059
0.6825 Remote Similarity NPC143810
0.6825 Remote Similarity NPC5698
0.6825 Remote Similarity NPC83838
0.6818 Remote Similarity NPC61503
0.6812 Remote Similarity NPC189745
0.6812 Remote Similarity NPC471781
0.6812 Remote Similarity NPC34834
0.6806 Remote Similarity NPC170148
0.68 Remote Similarity NPC474894
0.6786 Remote Similarity NPC157096
0.678 Remote Similarity NPC294358
0.678 Remote Similarity NPC40417
0.678 Remote Similarity NPC177112
0.678 Remote Similarity NPC71506
0.6774 Remote Similarity NPC470970
0.6769 Remote Similarity NPC474155
0.6769 Remote Similarity NPC473759
0.6765 Remote Similarity NPC208999
0.6761 Remote Similarity NPC190859
0.6761 Remote Similarity NPC27395
0.6761 Remote Similarity NPC329090
0.6757 Remote Similarity NPC328714
0.6724 Remote Similarity NPC225974
0.6721 Remote Similarity NPC130209
0.6721 Remote Similarity NPC477725
0.6721 Remote Similarity NPC473910
0.6721 Remote Similarity NPC473721
0.6721 Remote Similarity NPC475353
0.6721 Remote Similarity NPC148216
0.6721 Remote Similarity NPC473725
0.6721 Remote Similarity NPC474644
0.6721 Remote Similarity NPC477726
0.6721 Remote Similarity NPC148163
0.6721 Remote Similarity NPC473896
0.6721 Remote Similarity NPC473735
0.6719 Remote Similarity NPC321919
0.6719 Remote Similarity NPC252809
0.6719 Remote Similarity NPC81896
0.6719 Remote Similarity NPC323153
0.6716 Remote Similarity NPC83965
0.6714 Remote Similarity NPC471662
0.6714 Remote Similarity NPC242001
0.6714 Remote Similarity NPC472254
0.6714 Remote Similarity NPC477087
0.6714 Remote Similarity NPC477086
0.6712 Remote Similarity NPC130136
0.6712 Remote Similarity NPC84360
0.6711 Remote Similarity NPC472465
0.6711 Remote Similarity NPC30166
0.6711 Remote Similarity NPC20072
0.6667 Remote Similarity NPC209279
0.6667 Remote Similarity NPC88079
0.6667 Remote Similarity NPC319090
0.6667 Remote Similarity NPC194586
0.6667 Remote Similarity NPC180871
0.6667 Remote Similarity NPC68889
0.6667 Remote Similarity NPC74722
0.6667 Remote Similarity NPC269877

  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 NPC281590 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
0.7419 Intermediate Similarity NPD368 Approved
0.7222 Intermediate Similarity NPD4265 Approved
0.7042 Intermediate Similarity NPD6933 Approved
0.6761 Remote Similarity NPD6926 Approved
0.6761 Remote Similarity NPD6924 Approved
0.6721 Remote Similarity NPD342 Phase 1
0.6667 Remote Similarity NPD3197 Phase 1
0.6667 Remote Similarity NPD6922 Approved
0.6667 Remote Similarity NPD6923 Approved
0.6571 Remote Similarity NPD7144 Approved
0.6571 Remote Similarity NPD7143 Approved
0.6486 Remote Similarity NPD6932 Approved
0.6479 Remote Similarity NPD7150 Approved
0.6479 Remote Similarity NPD7151 Approved
0.6479 Remote Similarity NPD7152 Approved
0.6471 Remote Similarity NPD7331 Phase 2
0.6462 Remote Similarity NPD4246 Clinical (unspecified phase)
0.6447 Remote Similarity NPD7525 Registered
0.6438 Remote Similarity NPD8264 Approved
0.64 Remote Similarity NPD7322 Clinical (unspecified phase)
0.6389 Remote Similarity NPD4732 Discontinued
0.6324 Remote Similarity NPD2685 Clinical (unspecified phase)
0.6316 Remote Similarity NPD6683 Phase 2
0.6296 Remote Similarity NPD7524 Approved
0.6267 Remote Similarity NPD5776 Phase 2
0.6267 Remote Similarity NPD6925 Approved
0.6234 Remote Similarity NPD7509 Discontinued
0.6234 Remote Similarity NPD6931 Approved
0.6234 Remote Similarity NPD7332 Phase 2
0.6234 Remote Similarity NPD6930 Phase 2
0.6234 Remote Similarity NPD4821 Approved
0.6234 Remote Similarity NPD4819 Approved
0.6234 Remote Similarity NPD7514 Phase 3
0.6234 Remote Similarity NPD4822 Approved
0.6234 Remote Similarity NPD4820 Approved
0.6216 Remote Similarity NPD7339 Approved
0.6216 Remote Similarity NPD6942 Approved
0.6203 Remote Similarity NPD6695 Phase 3
0.6184 Remote Similarity NPD7145 Approved
0.6184 Remote Similarity NPD5784 Clinical (unspecified phase)
0.6154 Remote Similarity NPD5369 Approved
0.6154 Remote Similarity NPD6109 Phase 1
0.6154 Remote Similarity NPD6898 Phase 1
0.6133 Remote Similarity NPD3701 Clinical (unspecified phase)
0.6125 Remote Similarity NPD7338 Clinical (unspecified phase)
0.6104 Remote Similarity NPD6929 Approved
0.6104 Remote Similarity NPD7645 Phase 2
0.6094 Remote Similarity NPD4219 Approved
0.6026 Remote Similarity NPD5368 Approved
0.6026 Remote Similarity NPD8259 Clinical (unspecified phase)
0.6 Remote Similarity NPD5362 Discontinued
0.6 Remote Similarity NPD5331 Approved
0.6 Remote Similarity NPD6110 Phase 1
0.6 Remote Similarity NPD5332 Approved
0.6 Remote Similarity NPD7154 Phase 3
0.5974 Remote Similarity NPD4271 Approved
0.5974 Remote Similarity NPD4268 Approved
0.5949 Remote Similarity NPD6902 Approved
0.5949 Remote Similarity NPD4790 Discontinued
0.5915 Remote Similarity NPD4247 Clinical (unspecified phase)
0.5909 Remote Similarity NPD585 Clinical (unspecified phase)
0.5904 Remote Similarity NPD7750 Discontinued
0.5882 Remote Similarity NPD46 Approved
0.5882 Remote Similarity NPD6698 Approved
0.5882 Remote Similarity NPD7838 Discovery
0.5875 Remote Similarity NPD4269 Approved
0.5875 Remote Similarity NPD4270 Approved
0.5875 Remote Similarity NPD6435 Approved
0.5857 Remote Similarity NPD7341 Phase 2
0.5854 Remote Similarity NPD6893 Approved
0.5854 Remote Similarity NPD6082 Clinical (unspecified phase)
0.5823 Remote Similarity NPD4252 Approved
0.5823 Remote Similarity NPD5790 Clinical (unspecified phase)
0.5814 Remote Similarity NPD7983 Approved
0.5811 Remote Similarity NPD4243 Approved
0.5797 Remote Similarity NPD3210 Clinical (unspecified phase)
0.5781 Remote Similarity NPD3195 Phase 2
0.5781 Remote Similarity NPD4266 Approved
0.5781 Remote Similarity NPD3196 Approved
0.5781 Remote Similarity NPD3194 Approved
0.5763 Remote Similarity NPD39 Approved
0.5738 Remote Similarity NPD3173 Approved
0.5732 Remote Similarity NPD4786 Approved
0.5732 Remote Similarity NPD6400 Clinical (unspecified phase)
0.5679 Remote Similarity NPD3667 Approved
0.5663 Remote Similarity NPD5363 Approved
0.5658 Remote Similarity NPD4785 Approved
0.5658 Remote Similarity NPD4784 Approved
0.5632 Remote Similarity NPD7087 Discontinued
0.5625 Remote Similarity NPD3172 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