Structure

Physi-Chem Properties

Molecular Weight:  660.52
Volume:  722.347
LogP:  3.93
LogD:  3.619
LogS:  -3.222
# Rotatable Bonds:  32
TPSA:  83.07
# H-Bond Aceptor:  9
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  9

MedChem Properties

QED Drug-Likeness Score:  0.054
Synthetic Accessibility Score:  5.351
Fsp3:  0.892
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  1
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.459
MDCK Permeability:  2.3533031708211638e-05
Pgp-inhibitor:  1.0
Pgp-substrate:  0.773
Human Intestinal Absorption (HIA):  0.034
20% Bioavailability (F20%):  0.06
30% Bioavailability (F30%):  0.222

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.037
Plasma Protein Binding (PPB):  91.94441223144531%
Volume Distribution (VD):  0.944
Pgp-substrate:  6.276811122894287%

ADMET: Metabolism

CYP1A2-inhibitor:  0.0
CYP1A2-substrate:  0.198
CYP2C19-inhibitor:  0.0
CYP2C19-substrate:  0.947
CYP2C9-inhibitor:  0.0
CYP2C9-substrate:  0.0
CYP2D6-inhibitor:  0.0
CYP2D6-substrate:  0.106
CYP3A4-inhibitor:  0.418
CYP3A4-substrate:  0.905

ADMET: Excretion

Clearance (CL):  6.492
Half-life (T1/2):  0.015

ADMET: Toxicity

hERG Blockers:  0.779
Human Hepatotoxicity (H-HT):  0.418
Drug-inuced Liver Injury (DILI):  0.001
AMES Toxicity:  0.092
Rat Oral Acute Toxicity:  0.003
Maximum Recommended Daily Dose:  0.999
Skin Sensitization:  0.992
Carcinogencity:  0.661
Eye Corrosion:  0.232
Eye Irritation:  0.694
Respiratory Toxicity:  0.486

Download Data

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

  Natural Product: NPC226872

Natural Product ID:  NPC226872
Common Name*:   (4S,6S,8S,10S,12S,14S,16S,18S,20S,21E)-4,6,8,10,12,14,16,18,20-Nonamethoxy-21-Methylheptacosa-1,21-Diene
IUPAC Name:   (4S,6S,8S,10S,12S,14S,16S,18S,20S,21E)-4,6,8,10,12,14,16,18,20-nonamethoxy-21-methylheptacosa-1,21-diene
Synonyms:  
Standard InCHIKey:  KMIPEPBLCMHZOA-UIIBQYNYSA-N
Standard InCHI:  InChI=1S/C37H72O9/c1-13-15-16-17-19-28(3)37(46-12)27-36(45-11)26-35(44-10)25-34(43-9)24-33(42-8)23-32(41-7)22-31(40-6)21-30(39-5)20-29(38-4)18-14-2/h14,19,29-37H,2,13,15-18,20-27H2,1,3-12H3/b28-19+/t29-,30-,31-,32-,33-,34-,35-,36-,37-/m0/s1
SMILES:  CCCCC/C=C(/[C@H](C[C@H](C[C@H](C[C@H](C[C@H](C[C@H](C[C@H](C[C@H](C[C@H](CC=C)OC)OC)OC)OC)OC)OC)OC)OC)OC)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL446930
PubChem CID:   10439352
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000254] Ethers
          • [CHEMONTID:0001167] Dialkyl ethers

*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
NPO11960 Myriastra clavosa Species n.a. n.a. n.a. Philippines n.a. PMID[12193033]
NPO11960 Myriastra clavosa Species n.a. n.a. n.a. n.a. n.a. PMID[12350152]
NPO11960 Myriastra clavosa Species n.a. n.a. 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
NPT393 Cell Line HCT-116 Homo sapiens IC50 = 86000.0 nM PMID[572913]

☑ 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 NPC226872 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 NPC154908
1.0 High Similarity NPC158368
1.0 High Similarity NPC252851
0.9643 High Similarity NPC23418
0.7714 Intermediate Similarity NPC477204
0.7606 Intermediate Similarity NPC327041
0.7606 Intermediate Similarity NPC285840
0.7429 Intermediate Similarity NPC477084
0.7429 Intermediate Similarity NPC475762
0.7397 Intermediate Similarity NPC477203
0.7324 Intermediate Similarity NPC477085
0.7324 Intermediate Similarity NPC327383
0.7324 Intermediate Similarity NPC329914
0.7324 Intermediate Similarity NPC185186
0.726 Intermediate Similarity NPC469880
0.726 Intermediate Similarity NPC477202
0.7237 Intermediate Similarity NPC8538
0.7237 Intermediate Similarity NPC184208
0.7213 Intermediate Similarity NPC474496
0.7183 Intermediate Similarity NPC477087
0.7183 Intermediate Similarity NPC477086
0.7143 Intermediate Similarity NPC269841
0.7105 Intermediate Similarity NPC470147
0.7105 Intermediate Similarity NPC133226
0.7083 Intermediate Similarity NPC329890
0.7077 Intermediate Similarity NPC474267
0.7042 Intermediate Similarity NPC476012
0.7027 Intermediate Similarity NPC188860
0.7013 Intermediate Similarity NPC315731
0.7 Intermediate Similarity NPC475760
0.7 Intermediate Similarity NPC305698
0.6974 Remote Similarity NPC470148
0.6974 Remote Similarity NPC470149
0.6974 Remote Similarity NPC180725
0.6974 Remote Similarity NPC139712
0.697 Remote Similarity NPC127824
0.6957 Remote Similarity NPC284447
0.6933 Remote Similarity NPC84360
0.6933 Remote Similarity NPC474026
0.6933 Remote Similarity NPC233071
0.6923 Remote Similarity NPC10080
0.6923 Remote Similarity NPC123908
0.6912 Remote Similarity NPC477457
0.6912 Remote Similarity NPC477456
0.6901 Remote Similarity NPC472947
0.6901 Remote Similarity NPC101622
0.6885 Remote Similarity NPC474495
0.6885 Remote Similarity NPC473672
0.6883 Remote Similarity NPC474739
0.6857 Remote Similarity NPC259299
0.6857 Remote Similarity NPC73603
0.6842 Remote Similarity NPC248775
0.6818 Remote Similarity NPC122239
0.6818 Remote Similarity NPC143810
0.6818 Remote Similarity NPC83838
0.6806 Remote Similarity NPC4299
0.6806 Remote Similarity NPC469660
0.6806 Remote Similarity NPC476037
0.68 Remote Similarity NPC236228
0.68 Remote Similarity NPC256720
0.6769 Remote Similarity NPC470970
0.6753 Remote Similarity NPC476701
0.6753 Remote Similarity NPC473947
0.6753 Remote Similarity NPC477088
0.675 Remote Similarity NPC186155
0.675 Remote Similarity NPC78673
0.675 Remote Similarity NPC160517
0.6716 Remote Similarity NPC299730
0.6711 Remote Similarity NPC475711
0.6709 Remote Similarity NPC477385
0.6709 Remote Similarity NPC477390
0.6707 Remote Similarity NPC199382
0.6667 Remote Similarity NPC74722
0.6667 Remote Similarity NPC226848
0.6667 Remote Similarity NPC304690
0.6627 Remote Similarity NPC20339
0.6627 Remote Similarity NPC40376
0.6627 Remote Similarity NPC280621
0.6627 Remote Similarity NPC21208
0.6627 Remote Similarity NPC233551
0.6627 Remote Similarity NPC48338
0.6623 Remote Similarity NPC181838
0.6623 Remote Similarity NPC137345
0.6623 Remote Similarity NPC477089
0.6622 Remote Similarity NPC474705
0.662 Remote Similarity NPC472266
0.6615 Remote Similarity NPC471960
0.6615 Remote Similarity NPC477661
0.6615 Remote Similarity NPC475384
0.6615 Remote Similarity NPC470968
0.6615 Remote Similarity NPC470969
0.6615 Remote Similarity NPC161838
0.6615 Remote Similarity NPC473847
0.6615 Remote Similarity NPC470966
0.6615 Remote Similarity NPC470967
0.6588 Remote Similarity NPC476084
0.6588 Remote Similarity NPC206679
0.6588 Remote Similarity NPC114172
0.6588 Remote Similarity NPC471324
0.6588 Remote Similarity NPC476075
0.6585 Remote Similarity NPC47220
0.6585 Remote Similarity NPC186332
0.6585 Remote Similarity NPC61527
0.6579 Remote Similarity NPC301525
0.6575 Remote Similarity NPC129630
0.6567 Remote Similarity NPC159650
0.6567 Remote Similarity NPC22897
0.6562 Remote Similarity NPC256209
0.6562 Remote Similarity NPC49059
0.6557 Remote Similarity NPC98284
0.6538 Remote Similarity NPC86971
0.6538 Remote Similarity NPC471537
0.6538 Remote Similarity NPC1180
0.6533 Remote Similarity NPC24590
0.6533 Remote Similarity NPC471525
0.6528 Remote Similarity NPC272961
0.6528 Remote Similarity NPC218477
0.6522 Remote Similarity NPC473508
0.6522 Remote Similarity NPC54925
0.6515 Remote Similarity NPC52012
0.6515 Remote Similarity NPC471277
0.6515 Remote Similarity NPC471279
0.6512 Remote Similarity NPC159092
0.6512 Remote Similarity NPC109406
0.6506 Remote Similarity NPC178215
0.6506 Remote Similarity NPC477959
0.6494 Remote Similarity NPC97516
0.6486 Remote Similarity NPC84038
0.6479 Remote Similarity NPC248125
0.6471 Remote Similarity NPC177668
0.6471 Remote Similarity NPC239517
0.6463 Remote Similarity NPC477014
0.6463 Remote Similarity NPC322529
0.6463 Remote Similarity NPC477013
0.6463 Remote Similarity NPC329838
0.6463 Remote Similarity NPC120398
0.6463 Remote Similarity NPC329615
0.6463 Remote Similarity NPC471494
0.6463 Remote Similarity NPC471567
0.6462 Remote Similarity NPC473735
0.6462 Remote Similarity NPC475353
0.6462 Remote Similarity NPC477726
0.6462 Remote Similarity NPC473721
0.6462 Remote Similarity NPC473896
0.6462 Remote Similarity NPC477725
0.6462 Remote Similarity NPC223604
0.6462 Remote Similarity NPC473910
0.6462 Remote Similarity NPC473725
0.6456 Remote Similarity NPC190008
0.6456 Remote Similarity NPC127295
0.6456 Remote Similarity NPC163362
0.6456 Remote Similarity NPC469802
0.6438 Remote Similarity NPC475004
0.6429 Remote Similarity NPC34883
0.6429 Remote Similarity NPC320458
0.6429 Remote Similarity NPC25747
0.6429 Remote Similarity NPC89001
0.6429 Remote Similarity NPC473905
0.6429 Remote Similarity NPC148233
0.642 Remote Similarity NPC253801
0.641 Remote Similarity NPC474005
0.6406 Remote Similarity NPC26102
0.6406 Remote Similarity NPC477724
0.6406 Remote Similarity NPC187361
0.64 Remote Similarity NPC222244
0.64 Remote Similarity NPC55652
0.64 Remote Similarity NPC16349
0.6389 Remote Similarity NPC163290
0.6386 Remote Similarity NPC231096
0.6386 Remote Similarity NPC475581
0.6386 Remote Similarity NPC47937
0.6386 Remote Similarity NPC142117
0.6386 Remote Similarity NPC103523
0.6386 Remote Similarity NPC240695
0.6386 Remote Similarity NPC69082
0.6386 Remote Similarity NPC477015
0.6386 Remote Similarity NPC102996
0.6386 Remote Similarity NPC25703
0.6386 Remote Similarity NPC282815
0.6386 Remote Similarity NPC477389
0.6386 Remote Similarity NPC219652
0.6386 Remote Similarity NPC107717
0.6386 Remote Similarity NPC279267
0.6386 Remote Similarity NPC137253
0.6386 Remote Similarity NPC208473
0.6386 Remote Similarity NPC62118
0.6386 Remote Similarity NPC171174
0.6386 Remote Similarity NPC473840
0.6386 Remote Similarity NPC477387
0.6386 Remote Similarity NPC114694
0.6386 Remote Similarity NPC232555
0.6386 Remote Similarity NPC309211
0.6386 Remote Similarity NPC134865
0.6377 Remote Similarity NPC325929
0.6377 Remote Similarity NPC271282
0.6377 Remote Similarity NPC66460
0.6375 Remote Similarity NPC469469
0.6375 Remote Similarity NPC471661
0.6375 Remote Similarity NPC473339
0.6375 Remote Similarity NPC471552

  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 NPC226872 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
0.6667 Remote Similarity NPD7838 Discovery
0.6338 Remote Similarity NPD2685 Clinical (unspecified phase)
0.6279 Remote Similarity NPD46 Approved
0.6279 Remote Similarity NPD6698 Approved
0.6207 Remote Similarity NPD7983 Approved
0.6094 Remote Similarity NPD6927 Phase 3
0.6066 Remote Similarity NPD4265 Approved
0.6026 Remote Similarity NPD8039 Approved
0.5978 Remote Similarity NPD8029 Clinical (unspecified phase)
0.5974 Remote Similarity NPD4732 Discontinued
0.5946 Remote Similarity NPD4247 Clinical (unspecified phase)
0.5942 Remote Similarity NPD585 Clinical (unspecified phase)
0.5938 Remote Similarity NPD2268 Discontinued
0.593 Remote Similarity NPD4251 Approved
0.593 Remote Similarity NPD4250 Approved
0.5854 Remote Similarity NPD7514 Phase 3
0.5854 Remote Similarity NPD7332 Phase 2
0.5854 Remote Similarity NPD5790 Clinical (unspecified phase)
0.5833 Remote Similarity NPD7154 Phase 3
0.5833 Remote Similarity NPD6695 Phase 3
0.5823 Remote Similarity NPD8264 Approved
0.5814 Remote Similarity NPD4249 Approved
0.5811 Remote Similarity NPD6108 Clinical (unspecified phase)
0.5802 Remote Similarity NPD4268 Approved
0.5802 Remote Similarity NPD4271 Approved
0.5802 Remote Similarity NPD7145 Approved
0.5783 Remote Similarity NPD6902 Approved
0.5775 Remote Similarity NPD4246 Clinical (unspecified phase)
0.5765 Remote Similarity NPD7338 Clinical (unspecified phase)
0.5761 Remote Similarity NPD7839 Suspended
0.5753 Remote Similarity NPD5325 Clinical (unspecified phase)
0.5747 Remote Similarity NPD7750 Discontinued
0.5745 Remote Similarity NPD6648 Approved
0.5732 Remote Similarity NPD6929 Approved
0.573 Remote Similarity NPD8522 Clinical (unspecified phase)
0.5698 Remote Similarity NPD1733 Clinical (unspecified phase)
0.5684 Remote Similarity NPD5344 Discontinued
0.5679 Remote Similarity NPD6925 Approved
0.5679 Remote Similarity NPD5776 Phase 2
0.5679 Remote Similarity NPD6932 Approved
0.5663 Remote Similarity NPD6931 Approved
0.5663 Remote Similarity NPD4821 Approved
0.5663 Remote Similarity NPD4820 Approved
0.5663 Remote Similarity NPD4822 Approved
0.5663 Remote Similarity NPD6930 Phase 2
0.5663 Remote Similarity NPD4819 Approved
0.5647 Remote Similarity NPD5362 Discontinued
0.5616 Remote Similarity NPD3210 Clinical (unspecified phase)
0.5606 Remote Similarity NPD28 Approved
0.5606 Remote Similarity NPD29 Approved
0.5604 Remote Similarity NPD5779 Approved
0.5604 Remote Similarity NPD5778 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