Structure

Physi-Chem Properties

Molecular Weight:  487.27
Volume:  500.803
LogP:  3.206
LogD:  2.883
LogS:  -4.335
# Rotatable Bonds:  17
TPSA:  112.93
# H-Bond Aceptor:  7
# H-Bond Donor:  3
# Rings:  1
# Heavy Atoms:  8

MedChem Properties

QED Drug-Likeness Score:  0.133
Synthetic Accessibility Score:  4.552
Fsp3:  0.8
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  2
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.635
MDCK Permeability:  6.232968007680029e-05
Pgp-inhibitor:  0.993
Pgp-substrate:  0.006
Human Intestinal Absorption (HIA):  0.717
20% Bioavailability (F20%):  0.681
30% Bioavailability (F30%):  0.351

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.947
Plasma Protein Binding (PPB):  95.65132904052734%
Volume Distribution (VD):  0.286
Pgp-substrate:  3.73144268989563%

ADMET: Metabolism

CYP1A2-inhibitor:  0.011
CYP1A2-substrate:  0.096
CYP2C19-inhibitor:  0.099
CYP2C19-substrate:  0.318
CYP2C9-inhibitor:  0.152
CYP2C9-substrate:  0.082
CYP2D6-inhibitor:  0.011
CYP2D6-substrate:  0.235
CYP3A4-inhibitor:  0.771
CYP3A4-substrate:  0.192

ADMET: Excretion

Clearance (CL):  5.499
Half-life (T1/2):  0.722

ADMET: Toxicity

hERG Blockers:  0.057
Human Hepatotoxicity (H-HT):  0.409
Drug-inuced Liver Injury (DILI):  0.066
AMES Toxicity:  0.129
Rat Oral Acute Toxicity:  0.121
Maximum Recommended Daily Dose:  0.908
Skin Sensitization:  0.482
Carcinogencity:  0.115
Eye Corrosion:  0.003
Eye Irritation:  0.013
Respiratory Toxicity:  0.275

Download Data

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

  Natural Product: NPC323532

Natural Product ID:  NPC323532
Common Name*:   Malyngamide
IUPAC Name:   (E,7S)-N-[(E)-3-chloro-2-[(1S,2R,3R,5R)-2,3,5-trihydroxy-2-methyl-6-oxocyclohexyl]prop-2-enyl]-7-methoxytetradec-4-enamide
Synonyms:   Malyngamide
Standard InCHIKey:  OEGLIHPBLJQCGW-DRBFKITJSA-N
Standard InCHI:  InChI=1S/C25H42ClNO6/c1-4-5-6-7-9-12-19(33-3)13-10-8-11-14-22(30)27-17-18(16-26)23-24(31)20(28)15-21(29)25(23,2)32/h8,10,16,19-21,23,28-29,32H,4-7,9,11-15,17H2,1-3H3,(H,27,30)/b10-8+,18-16-/t19-,20+,21+,23+,25-/m0/s1
SMILES:  CCCCCCCC(CC=CCCC(=O)NCC(=CCl)C1C(=O)C(CC(C1(C)O)O)O)OC
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1669189
PubChem CID:   51354252
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001549] Monoterpenoids
          • [CHEMONTID:0001563] Monocyclic monoterpenoids

*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
NPO30527 Lyngbya Genus Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[14695793]
NPO30527 Lyngbya Genus Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[18693761]
NPO30527 Lyngbya Genus Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[21155594]
NPO30527 Lyngbya Genus Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[21650153]
NPO30527 Lyngbya Genus Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[24111939]

☑ 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
NPT113 Cell Line RAW264.7 Mus musculus IC50 = 8000.0 nM PMID[515234]
NPT113 Cell Line RAW264.7 Mus musculus Survival = 94.0 % PMID[515234]
NPT397 Cell Line NCI-H460 Homo sapiens IC50 = 27300.0 nM PMID[515234]

☑ 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 NPC323532 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
0.8655 High Similarity NPC280498
0.7949 Intermediate Similarity NPC46764
0.7462 Intermediate Similarity NPC164476
0.7462 Intermediate Similarity NPC121601
0.7462 Intermediate Similarity NPC471471
0.7273 Intermediate Similarity NPC474725
0.725 Intermediate Similarity NPC475800
0.7133 Intermediate Similarity NPC475837
0.7027 Intermediate Similarity NPC262026
0.7007 Intermediate Similarity NPC472430
0.6923 Remote Similarity NPC233770
0.6923 Remote Similarity NPC77481
0.6864 Remote Similarity NPC236176
0.6847 Remote Similarity NPC136114
0.6812 Remote Similarity NPC472428
0.6774 Remote Similarity NPC70235
0.6724 Remote Similarity NPC314500
0.6715 Remote Similarity NPC470185
0.6642 Remote Similarity NPC204639
0.6641 Remote Similarity NPC477266
0.664 Remote Similarity NPC168733
0.6639 Remote Similarity NPC128501
0.6614 Remote Similarity NPC12270
0.6614 Remote Similarity NPC146945
0.6614 Remote Similarity NPC171888
0.6612 Remote Similarity NPC473224
0.6577 Remote Similarity NPC67254
0.6562 Remote Similarity NPC7797
0.6535 Remote Similarity NPC92829
0.6529 Remote Similarity NPC234542
0.6512 Remote Similarity NPC7921
0.6512 Remote Similarity NPC208998
0.6512 Remote Similarity NPC122404
0.6508 Remote Similarity NPC307903
0.6508 Remote Similarity NPC140251
0.65 Remote Similarity NPC279722
0.6489 Remote Similarity NPC122033
0.6489 Remote Similarity NPC97908
0.6489 Remote Similarity NPC287343
0.6489 Remote Similarity NPC474654
0.6489 Remote Similarity NPC470854
0.648 Remote Similarity NPC166607
0.648 Remote Similarity NPC473252
0.6475 Remote Similarity NPC233932
0.6471 Remote Similarity NPC258674
0.6471 Remote Similarity NPC103527
0.6462 Remote Similarity NPC247069
0.6457 Remote Similarity NPC133729
0.6452 Remote Similarity NPC191892
0.6452 Remote Similarity NPC215988
0.6444 Remote Similarity NPC16709
0.6444 Remote Similarity NPC473802
0.6439 Remote Similarity NPC251310
0.6434 Remote Similarity NPC476269
0.6423 Remote Similarity NPC204556
0.6417 Remote Similarity NPC272617
0.6412 Remote Similarity NPC207217
0.6412 Remote Similarity NPC179626
0.64 Remote Similarity NPC14537
0.64 Remote Similarity NPC284865
0.64 Remote Similarity NPC475036
0.64 Remote Similarity NPC259476
0.64 Remote Similarity NPC160843
0.6397 Remote Similarity NPC473919
0.6397 Remote Similarity NPC473709
0.6393 Remote Similarity NPC152480
0.6385 Remote Similarity NPC73300
0.6385 Remote Similarity NPC198539
0.6385 Remote Similarity NPC108721
0.6378 Remote Similarity NPC289702
0.6378 Remote Similarity NPC208461
0.6377 Remote Similarity NPC477352
0.6371 Remote Similarity NPC478176
0.637 Remote Similarity NPC188222
0.637 Remote Similarity NPC282003
0.637 Remote Similarity NPC310035
0.6364 Remote Similarity NPC470775
0.6364 Remote Similarity NPC477116
0.6364 Remote Similarity NPC176513
0.6364 Remote Similarity NPC476190
0.6364 Remote Similarity NPC27999
0.6364 Remote Similarity NPC216335
0.6357 Remote Similarity NPC96425
0.6356 Remote Similarity NPC469464
0.635 Remote Similarity NPC470973
0.635 Remote Similarity NPC471939
0.6349 Remote Similarity NPC472615
0.6349 Remote Similarity NPC271269
0.6349 Remote Similarity NPC154601
0.6348 Remote Similarity NPC79573
0.6341 Remote Similarity NPC46761
0.6336 Remote Similarity NPC80650
0.6336 Remote Similarity NPC24462
0.6328 Remote Similarity NPC87335
0.6328 Remote Similarity NPC163004
0.6328 Remote Similarity NPC42662
0.6328 Remote Similarity NPC473578
0.6324 Remote Similarity NPC303006
0.632 Remote Similarity NPC320294
0.632 Remote Similarity NPC117185
0.6319 Remote Similarity NPC476558
0.6316 Remote Similarity NPC471118
0.6316 Remote Similarity NPC471121
0.6316 Remote Similarity NPC204552
0.6316 Remote Similarity NPC188667
0.6316 Remote Similarity NPC17772
0.6311 Remote Similarity NPC273269
0.6311 Remote Similarity NPC170978
0.6308 Remote Similarity NPC90769
0.6304 Remote Similarity NPC471940
0.6299 Remote Similarity NPC165873
0.6299 Remote Similarity NPC251330
0.6296 Remote Similarity NPC477046
0.6296 Remote Similarity NPC102822
0.6296 Remote Similarity NPC472401
0.6294 Remote Similarity NPC145899
0.6293 Remote Similarity NPC475753
0.629 Remote Similarity NPC470184
0.6288 Remote Similarity NPC328374
0.6288 Remote Similarity NPC40632
0.6288 Remote Similarity NPC251236
0.6288 Remote Similarity NPC96312
0.6279 Remote Similarity NPC140409
0.6279 Remote Similarity NPC11491
0.6279 Remote Similarity NPC156248
0.6279 Remote Similarity NPC476290
0.6277 Remote Similarity NPC469494
0.627 Remote Similarity NPC472616
0.6269 Remote Similarity NPC470186
0.6269 Remote Similarity NPC469488
0.6268 Remote Similarity NPC78189
0.6268 Remote Similarity NPC76999
0.626 Remote Similarity NPC106479
0.626 Remote Similarity NPC49451
0.6259 Remote Similarity NPC477793
0.6259 Remote Similarity NPC476091
0.6259 Remote Similarity NPC476078
0.6259 Remote Similarity NPC329919
0.625 Remote Similarity NPC29827
0.625 Remote Similarity NPC230889
0.625 Remote Similarity NPC475150
0.625 Remote Similarity NPC61275
0.625 Remote Similarity NPC19464
0.6241 Remote Similarity NPC147707
0.6241 Remote Similarity NPC476712
0.6241 Remote Similarity NPC476713
0.6241 Remote Similarity NPC471117
0.6241 Remote Similarity NPC471120
0.6241 Remote Similarity NPC296822
0.6241 Remote Similarity NPC201968
0.624 Remote Similarity NPC474709
0.6239 Remote Similarity NPC298904
0.6232 Remote Similarity NPC217901
0.6232 Remote Similarity NPC225049
0.6231 Remote Similarity NPC170294
0.6231 Remote Similarity NPC476023
0.6231 Remote Similarity NPC157476
0.6231 Remote Similarity NPC474229
0.6224 Remote Similarity NPC75318
0.6222 Remote Similarity NPC112038
0.6222 Remote Similarity NPC477140
0.6222 Remote Similarity NPC477143
0.6222 Remote Similarity NPC475003
0.622 Remote Similarity NPC128828
0.6218 Remote Similarity NPC472325
0.6214 Remote Similarity NPC162495
0.6212 Remote Similarity NPC473798
0.6212 Remote Similarity NPC117712
0.6212 Remote Similarity NPC50694
0.621 Remote Similarity NPC127408
0.621 Remote Similarity NPC291785
0.6207 Remote Similarity NPC243680
0.6207 Remote Similarity NPC200788
0.6204 Remote Similarity NPC472399
0.6198 Remote Similarity NPC478089
0.6198 Remote Similarity NPC196227
0.6194 Remote Similarity NPC200412
0.6194 Remote Similarity NPC297179
0.6194 Remote Similarity NPC120599
0.6194 Remote Similarity NPC470776
0.6194 Remote Similarity NPC156336
0.619 Remote Similarity NPC194323
0.619 Remote Similarity NPC474563
0.6187 Remote Similarity NPC475273
0.6187 Remote Similarity NPC168849
0.6183 Remote Similarity NPC275100
0.6183 Remote Similarity NPC469865
0.6183 Remote Similarity NPC473877
0.6183 Remote Similarity NPC474516
0.6183 Remote Similarity NPC280782
0.6179 Remote Similarity NPC272451
0.6179 Remote Similarity NPC473574
0.6179 Remote Similarity NPC20078
0.6176 Remote Similarity NPC469515
0.6172 Remote Similarity NPC144854
0.6172 Remote Similarity NPC3316
0.6172 Remote Similarity NPC474716
0.617 Remote Similarity NPC475389
0.617 Remote Similarity NPC475314
0.617 Remote Similarity NPC475606

  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 NPC323532 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
0.6639 Remote Similarity NPD3653 Clinical (unspecified phase)
0.6614 Remote Similarity NPD1719 Phase 1
0.6541 Remote Similarity NPD6921 Approved
0.6378 Remote Similarity NPD5345 Clinical (unspecified phase)
0.6349 Remote Similarity NPD5357 Phase 1
0.6279 Remote Similarity NPD6421 Discontinued
0.625 Remote Similarity NPD5781 Clinical (unspecified phase)
0.6154 Remote Similarity NPD4634 Approved
0.6136 Remote Similarity NPD4632 Approved
0.6096 Remote Similarity NPD6333 Approved
0.6096 Remote Similarity NPD6334 Approved
0.6083 Remote Similarity NPD3168 Discontinued
0.6071 Remote Similarity NPD8074 Phase 3
0.6 Remote Similarity NPD8415 Approved
0.5985 Remote Similarity NPD5215 Approved
0.5984 Remote Similarity NPD5779 Approved
0.5984 Remote Similarity NPD5778 Approved
0.5942 Remote Similarity NPD5983 Phase 2
0.5935 Remote Similarity NPD5282 Discontinued
0.5915 Remote Similarity NPD6033 Approved
0.5912 Remote Similarity NPD7100 Approved
0.5909 Remote Similarity NPD5169 Approved
0.5909 Remote Similarity NPD6420 Discontinued
0.5882 Remote Similarity NPD6009 Approved
0.587 Remote Similarity NPD6319 Approved
0.587 Remote Similarity NPD6054 Approved
0.5868 Remote Similarity NPD6101 Approved
0.5868 Remote Similarity NPD5764 Clinical (unspecified phase)
0.5867 Remote Similarity NPD8384 Approved
0.5865 Remote Similarity NPD5127 Approved
0.585 Remote Similarity NPD8387 Clinical (unspecified phase)
0.5839 Remote Similarity NPD6335 Approved
0.5827 Remote Similarity NPD4696 Approved
0.5827 Remote Similarity NPD5286 Approved
0.5827 Remote Similarity NPD6908 Approved
0.5827 Remote Similarity NPD5285 Approved
0.5827 Remote Similarity NPD6909 Approved
0.5797 Remote Similarity NPD4522 Approved
0.5794 Remote Similarity NPD4755 Approved
0.5786 Remote Similarity NPD6370 Approved
0.5781 Remote Similarity NPD5344 Discontinued
0.5772 Remote Similarity NPD7983 Approved
0.5772 Remote Similarity NPD6411 Approved
0.5766 Remote Similarity NPD7500 Approved
0.5758 Remote Similarity NPD5128 Approved
0.5758 Remote Similarity NPD6899 Approved
0.5758 Remote Similarity NPD6881 Approved
0.5755 Remote Similarity NPD6059 Approved
0.5746 Remote Similarity NPD6650 Approved
0.5746 Remote Similarity NPD5216 Approved
0.5746 Remote Similarity NPD7601 Clinical (unspecified phase)
0.5746 Remote Similarity NPD5217 Approved
0.5746 Remote Similarity NPD6649 Approved
0.5745 Remote Similarity NPD8328 Phase 3
0.5745 Remote Similarity NPD7604 Phase 2
0.5736 Remote Similarity NPD5226 Approved
0.5736 Remote Similarity NPD5224 Approved
0.5736 Remote Similarity NPD5225 Approved
0.5736 Remote Similarity NPD5211 Phase 2
0.5736 Remote Similarity NPD4633 Approved
0.5735 Remote Similarity NPD5167 Approved
0.5725 Remote Similarity NPD7641 Discontinued
0.5725 Remote Similarity NPD6675 Approved
0.5725 Remote Similarity NPD6313 Approved
0.5725 Remote Similarity NPD5739 Approved
0.5725 Remote Similarity NPD6314 Approved
0.5725 Remote Similarity NPD7128 Approved
0.5725 Remote Similarity NPD6402 Approved
0.5724 Remote Similarity NPD6914 Discontinued
0.5714 Remote Similarity NPD8274 Clinical (unspecified phase)
0.5714 Remote Similarity NPD6016 Approved
0.5714 Remote Similarity NPD7839 Suspended
0.5714 Remote Similarity NPD6015 Approved
0.5714 Remote Similarity NPD6373 Approved
0.5714 Remote Similarity NPD6372 Approved
0.5704 Remote Similarity NPD8341 Approved
0.5704 Remote Similarity NPD8340 Approved
0.5704 Remote Similarity NPD7492 Approved
0.5704 Remote Similarity NPD8299 Approved
0.5704 Remote Similarity NPD8297 Approved
0.5704 Remote Similarity NPD8342 Approved
0.5703 Remote Similarity NPD4700 Approved
0.5692 Remote Similarity NPD5174 Approved
0.5692 Remote Similarity NPD5175 Approved
0.5683 Remote Similarity NPD7101 Approved
0.5682 Remote Similarity NPD5697 Approved
0.5674 Remote Similarity NPD5988 Approved
0.5674 Remote Similarity NPD8080 Discontinued
0.5672 Remote Similarity NPD6883 Approved
0.5672 Remote Similarity NPD7102 Approved
0.5672 Remote Similarity NPD7290 Approved
0.5667 Remote Similarity NPD619 Phase 3
0.5664 Remote Similarity NPD6336 Discontinued
0.5664 Remote Similarity NPD8451 Approved
0.5664 Remote Similarity NPD6616 Approved
0.5659 Remote Similarity NPD5223 Approved
0.5652 Remote Similarity NPD8295 Clinical (unspecified phase)
0.5649 Remote Similarity NPD5141 Approved
0.5646 Remote Similarity NPD8338 Approved
0.5639 Remote Similarity NPD7320 Approved
0.5634 Remote Similarity NPD7642 Approved
0.563 Remote Similarity NPD8130 Phase 1
0.563 Remote Similarity NPD6869 Approved
0.563 Remote Similarity NPD6847 Approved
0.563 Remote Similarity NPD6617 Approved
0.5625 Remote Similarity NPD8448 Approved
0.5625 Remote Similarity NPD7078 Approved
0.5616 Remote Similarity NPD8391 Approved
0.5616 Remote Similarity NPD8390 Approved
0.5616 Remote Similarity NPD8392 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