Structure

Physi-Chem Properties

Molecular Weight:  350.18
Volume:  361.454
LogP:  1.261
LogD:  0.573
LogS:  -1.803
# Rotatable Bonds:  9
TPSA:  126.89
# H-Bond Aceptor:  7
# H-Bond Donor:  3
# Rings:  1
# Heavy Atoms:  7

MedChem Properties

QED Drug-Likeness Score:  0.387
Synthetic Accessibility Score:  4.025
Fsp3:  0.611
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  1
PAINS Alert:  1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.803
MDCK Permeability:  1.887170765257906e-05
Pgp-inhibitor:  0.119
Pgp-substrate:  0.245
Human Intestinal Absorption (HIA):  0.007
20% Bioavailability (F20%):  0.004
30% Bioavailability (F30%):  0.025

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.951
Plasma Protein Binding (PPB):  57.91499328613281%
Volume Distribution (VD):  0.295
Pgp-substrate:  57.97478485107422%

ADMET: Metabolism

CYP1A2-inhibitor:  0.009
CYP1A2-substrate:  0.123
CYP2C19-inhibitor:  0.023
CYP2C19-substrate:  0.064
CYP2C9-inhibitor:  0.021
CYP2C9-substrate:  0.098
CYP2D6-inhibitor:  0.002
CYP2D6-substrate:  0.063
CYP3A4-inhibitor:  0.036
CYP3A4-substrate:  0.359

ADMET: Excretion

Clearance (CL):  7.358
Half-life (T1/2):  0.545

ADMET: Toxicity

hERG Blockers:  0.009
Human Hepatotoxicity (H-HT):  0.104
Drug-inuced Liver Injury (DILI):  0.07
AMES Toxicity:  0.15
Rat Oral Acute Toxicity:  0.093
Maximum Recommended Daily Dose:  0.023
Skin Sensitization:  0.509
Carcinogencity:  0.424
Eye Corrosion:  0.004
Eye Irritation:  0.025
Respiratory Toxicity:  0.812

Download Data

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

  Natural Product: NPC133729

Natural Product ID:  NPC133729
Common Name*:   Daryamide A
IUPAC Name:   (2E,4E)-N-[(3S,4R)-3-(3-amino-3-oxopropyl)-3,4-dihydroxy-6-oxocyclohexen-1-yl]-7-methylocta-2,4-dienamide
Synonyms:  
Standard InCHIKey:  VLZVGRPEASVNDM-HMBRAYOKSA-N
Standard InCHI:  InChI=1S/C18H26N2O5/c1-12(2)6-4-3-5-7-17(24)20-13-11-18(25,9-8-16(19)23)15(22)10-14(13)21/h3-5,7,11-12,15,22,25H,6,8-10H2,1-2H3,(H2,19,23)(H,20,24)/b4-3+,7-5+/t15-,18+/m1/s1
SMILES:  CC(C/C=C/C=C/C(=NC1=C[C@@](O)(CCC(=N)O)[C@@H](CC1=O)O)O)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL450849
PubChem CID:   16099480
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0001831] Carbonyl compounds
          • [CHEMONTID:0000118] Ketones
            • [CHEMONTID:0003487] Cyclic ketones
              • [CHEMONTID:0004325] Cyclohexenones

*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
NPO32837 streptomyces strain cnq-085 Species Streptomycetaceae Bacteria n.a. n.a. n.a. PMID[17190455]

☑ 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 = 3.15 ug.mL-1 PMID[549980]
NPT20 Organism Candida albicans Candida albicans MIC = 62.5 ug.mL-1 PMID[549980]

☑ 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 NPC133729 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
0.8585 High Similarity NPC472615
0.8491 Intermediate Similarity NPC472616
0.8319 Intermediate Similarity NPC316325
0.7692 Intermediate Similarity NPC59751
0.7692 Intermediate Similarity NPC271621
0.7692 Intermediate Similarity NPC27413
0.7583 Intermediate Similarity NPC315915
0.7565 Intermediate Similarity NPC170375
0.754 Intermediate Similarity NPC314361
0.7458 Intermediate Similarity NPC7905
0.7458 Intermediate Similarity NPC315652
0.7436 Intermediate Similarity NPC5485
0.7355 Intermediate Similarity NPC473808
0.7333 Intermediate Similarity NPC296361
0.73 Intermediate Similarity NPC314854
0.73 Intermediate Similarity NPC313911
0.7155 Intermediate Similarity NPC307903
0.7155 Intermediate Similarity NPC140251
0.7143 Intermediate Similarity NPC473249
0.713 Intermediate Similarity NPC314500
0.7083 Intermediate Similarity NPC471645
0.7075 Intermediate Similarity NPC472614
0.7069 Intermediate Similarity NPC251330
0.7054 Intermediate Similarity NPC234542
0.704 Intermediate Similarity NPC16709
0.6991 Remote Similarity NPC473224
0.6983 Remote Similarity NPC271269
0.6857 Remote Similarity NPC477785
0.6857 Remote Similarity NPC477784
0.6857 Remote Similarity NPC477786
0.685 Remote Similarity NPC469494
0.6847 Remote Similarity NPC116930
0.6838 Remote Similarity NPC154601
0.6818 Remote Similarity NPC78189
0.6818 Remote Similarity NPC142838
0.681 Remote Similarity NPC474563
0.6791 Remote Similarity NPC230889
0.6783 Remote Similarity NPC313234
0.6783 Remote Similarity NPC316250
0.6777 Remote Similarity NPC469865
0.6757 Remote Similarity NPC472613
0.6752 Remote Similarity NPC14537
0.6746 Remote Similarity NPC469515
0.6695 Remote Similarity NPC473252
0.6692 Remote Similarity NPC477793
0.6692 Remote Similarity NPC329919
0.6639 Remote Similarity NPC476269
0.6602 Remote Similarity NPC471061
0.6589 Remote Similarity NPC204639
0.6581 Remote Similarity NPC128501
0.6574 Remote Similarity NPC187529
0.6529 Remote Similarity NPC473578
0.6525 Remote Similarity NPC233770
0.6525 Remote Similarity NPC77481
0.6525 Remote Similarity NPC316249
0.6514 Remote Similarity NPC258824
0.65 Remote Similarity NPC475800
0.65 Remote Similarity NPC315531
0.6475 Remote Similarity NPC476290
0.6471 Remote Similarity NPC74035
0.6457 Remote Similarity NPC323532
0.6446 Remote Similarity NPC475150
0.6435 Remote Similarity NPC175614
0.6429 Remote Similarity NPC476190
0.6429 Remote Similarity NPC475642
0.6418 Remote Similarity NPC96425
0.6415 Remote Similarity NPC470947
0.6415 Remote Similarity NPC470946
0.6415 Remote Similarity NPC470945
0.64 Remote Similarity NPC50694
0.6396 Remote Similarity NPC316186
0.6393 Remote Similarity NPC474725
0.6391 Remote Similarity NPC164476
0.6391 Remote Similarity NPC471471
0.6389 Remote Similarity NPC471595
0.6387 Remote Similarity NPC118902
0.6387 Remote Similarity NPC104161
0.6387 Remote Similarity NPC469980
0.6381 Remote Similarity NPC231739
0.6379 Remote Similarity NPC265662
0.6372 Remote Similarity NPC476705
0.6357 Remote Similarity NPC156379
0.6357 Remote Similarity NPC160688
0.6357 Remote Similarity NPC475383
0.6355 Remote Similarity NPC275766
0.6341 Remote Similarity NPC477997
0.6303 Remote Similarity NPC469598
0.6299 Remote Similarity NPC201968
0.6296 Remote Similarity NPC158411
0.6296 Remote Similarity NPC38796
0.6293 Remote Similarity NPC195645
0.6293 Remote Similarity NPC165332
0.6293 Remote Similarity NPC93271
0.6293 Remote Similarity NPC135576
0.6293 Remote Similarity NPC473291
0.6293 Remote Similarity NPC180722
0.629 Remote Similarity NPC29501
0.629 Remote Similarity NPC12270
0.6273 Remote Similarity NPC15807
0.6269 Remote Similarity NPC110294
0.6269 Remote Similarity NPC121601
0.6261 Remote Similarity NPC5418
0.626 Remote Similarity NPC24389
0.625 Remote Similarity NPC87189
0.625 Remote Similarity NPC228415
0.624 Remote Similarity NPC66108
0.6239 Remote Similarity NPC40812
0.6239 Remote Similarity NPC266842
0.6232 Remote Similarity NPC472430
0.6231 Remote Similarity NPC314293
0.623 Remote Similarity NPC266514
0.6226 Remote Similarity NPC478122
0.622 Remote Similarity NPC30196
0.6212 Remote Similarity NPC470653
0.6212 Remote Similarity NPC470650
0.6212 Remote Similarity NPC470654
0.6207 Remote Similarity NPC205546
0.6207 Remote Similarity NPC272050
0.6207 Remote Similarity NPC233273
0.6207 Remote Similarity NPC189764
0.6207 Remote Similarity NPC50902
0.6202 Remote Similarity NPC241050
0.6194 Remote Similarity NPC471586
0.6186 Remote Similarity NPC83895
0.6186 Remote Similarity NPC161855
0.6186 Remote Similarity NPC187761
0.6172 Remote Similarity NPC6531
0.6167 Remote Similarity NPC39996
0.616 Remote Similarity NPC475608
0.616 Remote Similarity NPC21713
0.6154 Remote Similarity NPC477143
0.6154 Remote Similarity NPC123141
0.6154 Remote Similarity NPC477140
0.6148 Remote Similarity NPC201128
0.6147 Remote Similarity NPC469833
0.6147 Remote Similarity NPC469838
0.6142 Remote Similarity NPC476813
0.6142 Remote Similarity NPC476814
0.6136 Remote Similarity NPC280498
0.6129 Remote Similarity NPC298484
0.6121 Remote Similarity NPC196227
0.6119 Remote Similarity NPC204556
0.6111 Remote Similarity NPC7797
0.6106 Remote Similarity NPC476706
0.6106 Remote Similarity NPC476708
0.6106 Remote Similarity NPC476707
0.6102 Remote Similarity NPC20066
0.6102 Remote Similarity NPC167380
0.6099 Remote Similarity NPC208725
0.6098 Remote Similarity NPC469853
0.6094 Remote Similarity NPC296043
0.6087 Remote Similarity NPC116726
0.6083 Remote Similarity NPC175531
0.608 Remote Similarity NPC113012
0.608 Remote Similarity NPC122926
0.6075 Remote Similarity NPC475994
0.6071 Remote Similarity NPC315395
0.6071 Remote Similarity NPC164393
0.6071 Remote Similarity NPC316426
0.6055 Remote Similarity NPC470298
0.605 Remote Similarity NPC261377
0.605 Remote Similarity NPC308567
0.605 Remote Similarity NPC300584
0.605 Remote Similarity NPC255592
0.6048 Remote Similarity NPC70235
0.6048 Remote Similarity NPC264819
0.6047 Remote Similarity NPC329216
0.6043 Remote Similarity NPC472428
0.6038 Remote Similarity NPC474197
0.6036 Remote Similarity NPC136114
0.6036 Remote Similarity NPC219966
0.6034 Remote Similarity NPC295204
0.6034 Remote Similarity NPC288240
0.6034 Remote Similarity NPC162205
0.6034 Remote Similarity NPC273579
0.6034 Remote Similarity NPC476049
0.6019 Remote Similarity NPC107848
0.6019 Remote Similarity NPC19900
0.6019 Remote Similarity NPC113363
0.6018 Remote Similarity NPC86005
0.6018 Remote Similarity NPC23622
0.6018 Remote Similarity NPC472007
0.6016 Remote Similarity NPC475918
0.6015 Remote Similarity NPC315783
0.6014 Remote Similarity NPC300912
0.6014 Remote Similarity NPC202166
0.6014 Remote Similarity NPC473261
0.6014 Remote Similarity NPC473262
0.6 Remote Similarity NPC475053
0.6 Remote Similarity NPC469464
0.6 Remote Similarity NPC166554
0.6 Remote Similarity NPC175585
0.6 Remote Similarity NPC477866
0.6 Remote Similarity NPC477865
0.6 Remote Similarity NPC265856
0.6 Remote Similarity NPC313670
0.6 Remote Similarity NPC473448
0.6 Remote Similarity NPC279186
0.6 Remote Similarity NPC316228
0.5984 Remote Similarity NPC60432

  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 NPC133729 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
0.8319 Intermediate Similarity NPD7500 Approved
0.8036 Intermediate Similarity NPD7116 Clinical (unspecified phase)
0.7565 Intermediate Similarity NPD7601 Clinical (unspecified phase)
0.7377 Intermediate Similarity NPD7623 Phase 3
0.7377 Intermediate Similarity NPD7624 Clinical (unspecified phase)
0.7154 Intermediate Similarity NPD7739 Clinical (unspecified phase)
0.7143 Intermediate Similarity NPD7747 Phase 1
0.7143 Intermediate Similarity NPD7746 Phase 1
0.68 Remote Similarity NPD7299 Clinical (unspecified phase)
0.6612 Remote Similarity NPD6421 Discontinued
0.6293 Remote Similarity NPD7839 Suspended
0.629 Remote Similarity NPD1719 Phase 1
0.626 Remote Similarity NPD6413 Approved
0.6172 Remote Similarity NPD7505 Discontinued
0.6126 Remote Similarity NPD5363 Approved
0.6119 Remote Similarity NPD8074 Phase 3
0.6087 Remote Similarity NPD7983 Approved
0.6015 Remote Similarity NPD7829 Approved
0.6015 Remote Similarity NPD7830 Approved
0.5985 Remote Similarity NPD6914 Discontinued
0.5952 Remote Similarity NPD6420 Discontinued
0.5926 Remote Similarity NPD8273 Phase 1
0.5897 Remote Similarity NPD5779 Approved
0.5897 Remote Similarity NPD5778 Approved
0.5896 Remote Similarity NPD7642 Approved
0.5878 Remote Similarity NPD7641 Discontinued
0.5865 Remote Similarity NPD8444 Approved
0.5862 Remote Similarity NPD5785 Approved
0.5856 Remote Similarity NPD4269 Approved
0.5856 Remote Similarity NPD4270 Approved
0.5854 Remote Similarity NPD2258 Approved
0.5854 Remote Similarity NPD2259 Approved
0.5852 Remote Similarity NPD8341 Approved
0.5852 Remote Similarity NPD8340 Approved
0.5852 Remote Similarity NPD8342 Approved
0.5852 Remote Similarity NPD8299 Approved
0.5818 Remote Similarity NPD4252 Approved
0.5785 Remote Similarity NPD8029 Clinical (unspecified phase)
0.578 Remote Similarity NPD3732 Approved
0.5755 Remote Similarity NPD8392 Approved
0.5755 Remote Similarity NPD8391 Approved
0.5755 Remote Similarity NPD8390 Approved
0.575 Remote Similarity NPD4228 Discovery
0.5738 Remote Similarity NPD6404 Discontinued
0.5726 Remote Similarity NPD46 Approved
0.5726 Remote Similarity NPD6698 Approved
0.5714 Remote Similarity NPD5282 Discontinued
0.5703 Remote Similarity NPD6371 Approved
0.5694 Remote Similarity NPD6333 Approved
0.5694 Remote Similarity NPD6334 Approved
0.5693 Remote Similarity NPD8451 Approved
0.5682 Remote Similarity NPD6935 Phase 3
0.5682 Remote Similarity NPD6936 Clinical (unspecified phase)
0.5672 Remote Similarity NPD2218 Phase 2
0.5672 Remote Similarity NPD2217 Approved
0.5664 Remote Similarity NPD6110 Phase 1
0.5652 Remote Similarity NPD8448 Approved
0.5652 Remote Similarity NPD5786 Approved
0.563 Remote Similarity NPD5781 Clinical (unspecified phase)
0.5625 Remote Similarity NPD5369 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