Structure

Physi-Chem Properties

Molecular Weight:  633.4
Volume:  629.104
LogP:  0.58
LogD:  1.185
LogS:  -2.09
# Rotatable Bonds:  3
TPSA:  175.53
# H-Bond Aceptor:  15
# H-Bond Donor:  5
# Rings:  4
# Heavy Atoms:  15

MedChem Properties

QED Drug-Likeness Score:  0.261
Synthetic Accessibility Score:  5.437
Fsp3:  0.8
Lipinski Rule-of-5:  Rejected
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.739
MDCK Permeability:  2.427698746032547e-06
Pgp-inhibitor:  0.955
Pgp-substrate:  0.99
Human Intestinal Absorption (HIA):  0.916
20% Bioavailability (F20%):  0.392
30% Bioavailability (F30%):  0.987

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.009
Plasma Protein Binding (PPB):  60.10848617553711%
Volume Distribution (VD):  0.828
Pgp-substrate:  66.79862976074219%

ADMET: Metabolism

CYP1A2-inhibitor:  0.0
CYP1A2-substrate:  0.027
CYP2C19-inhibitor:  0.023
CYP2C19-substrate:  0.118
CYP2C9-inhibitor:  0.017
CYP2C9-substrate:  0.072
CYP2D6-inhibitor:  0.0
CYP2D6-substrate:  0.025
CYP3A4-inhibitor:  0.372
CYP3A4-substrate:  0.197

ADMET: Excretion

Clearance (CL):  4.294
Half-life (T1/2):  0.393

ADMET: Toxicity

hERG Blockers:  0.025
Human Hepatotoxicity (H-HT):  0.994
Drug-inuced Liver Injury (DILI):  0.981
AMES Toxicity:  0.024
Rat Oral Acute Toxicity:  0.121
Maximum Recommended Daily Dose:  0.084
Skin Sensitization:  0.433
Carcinogencity:  0.83
Eye Corrosion:  0.003
Eye Irritation:  0.003
Respiratory Toxicity:  0.708

Download Data

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

  Natural Product: NPC301010

Natural Product ID:  NPC301010
Common Name*:   NYDALYAIISZVCH-WQRAYAPSSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  NYDALYAIISZVCH-WQRAYAPSSA-N
Standard InCHI:  InChI=1S/C30H51N9O6/c1-17(2)16-20-25(40)35-24(18(3)4)30(45)39-23(12-9-15-33-39)29(44)38-22(11-8-14-32-38)28(43)36(6)19(5)27(42)37-21(26(41)34-20)10-7-13-31-37/h17-24,31-33H,7-16H2,1-6H3,(H,34,41)(H,35,40)/t19-,20-,21+,22+,23-,24+/m0/s1
SMILES:  CC(C)C[C@H]1C(=N[C@H](C(C)C)C(=O)N2[C@@H](CCCN2)C(=O)N2[C@H](CCCN2)C(=O)N(C)[C@@H](C)C(=O)N2[C@H](CCCN2)C(=N1)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL3088122
PubChem CID:   76331743
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000064] Macrolactams

*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
NPO13391 Streptomyces hygroscopicus Species Streptomycetaceae Bacteria n.a. n.a. n.a. PMID[14563159]
NPO13391 Streptomyces hygroscopicus Species Streptomycetaceae Bacteria n.a. n.a. n.a. PMID[15844961]
NPO13391 Streptomyces hygroscopicus Species Streptomycetaceae Bacteria n.a. n.a. n.a. PMID[16378365]
NPO13391 Streptomyces hygroscopicus Species Streptomycetaceae Bacteria n.a. n.a. n.a. PMID[16453790]
NPO13391 Streptomyces hygroscopicus Species Streptomycetaceae Bacteria n.a. n.a. n.a. PMID[16724461]
NPO13391 Streptomyces hygroscopicus Species Streptomycetaceae Bacteria n.a. n.a. n.a. PMID[17632514]
NPO13391 Streptomyces hygroscopicus Species Streptomycetaceae Bacteria n.a. n.a. n.a. PMID[19231864]
NPO13391 Streptomyces hygroscopicus Species Streptomycetaceae Bacteria n.a. n.a. n.a. PMID[21486005]
NPO13391 Streptomyces hygroscopicus Species Streptomycetaceae Bacteria n.a. n.a. n.a. PMID[21504214]
NPO13391 Streptomyces hygroscopicus Species Streptomycetaceae Bacteria n.a. n.a. n.a. PMID[24224794]
NPO13391 Streptomyces hygroscopicus Species Streptomycetaceae Bacteria n.a. n.a. n.a. PMID[3170341]
NPO13391 Streptomyces hygroscopicus Species Streptomycetaceae Bacteria n.a. n.a. n.a. PMID[3819734]
NPO13391 Streptomyces hygroscopicus Species Streptomycetaceae Bacteria n.a. n.a. n.a. PMID[5549382]
NPO13391 Streptomyces hygroscopicus Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[TCMID]
NPO13391 Streptomyces hygroscopicus Species Streptomycetaceae Bacteria 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
NPT189 Cell Line Vero Chlorocebus aethiops IC50 = 24.2 ug.mL-1 PMID[479022]
NPT1118 Organism Streptococcus pneumoniae Streptococcus pneumoniae MIC>90 = 8.4 ug ml-1 PMID[479022]
NPT18 Organism Pseudomonas aeruginosa Pseudomonas aeruginosa MIC>90 > 10.0 ug ml-1 PMID[479022]
NPT1204 Organism Enterococcus faecalis ATCC 29212 Enterococcus faecalis ATCC 29212 MIC>90 = 8.0 ug ml-1 PMID[479022]
NPT88 Organism Mycobacterium tuberculosis Mycobacterium tuberculosis MBC90 = 19.5 ug ml-1 PMID[479022]
NPT790 Organism Mycobacterium tuberculosis H37Rv Mycobacterium tuberculosis H37Rv MBC90 > 50.0 ug ml-1 PMID[479022]
NPT88 Organism Mycobacterium tuberculosis Mycobacterium tuberculosis Ratio = 10.0 n.a. PMID[479022]
NPT790 Organism Mycobacterium tuberculosis H37Rv Mycobacterium tuberculosis H37Rv Ratio = 2.0 n.a. PMID[479022]
NPT88 Organism Mycobacterium tuberculosis Mycobacterium tuberculosis MIC>90 = 20.9 ug ml-1 PMID[479022]
NPT88 Organism Mycobacterium tuberculosis Mycobacterium tuberculosis MIC>90 = 19.1 ug ml-1 PMID[479022]
NPT790 Organism Mycobacterium tuberculosis H37Rv Mycobacterium tuberculosis H37Rv MIC>90 = 29.2 ug ml-1 PMID[479022]
NPT790 Organism Mycobacterium tuberculosis H37Rv Mycobacterium tuberculosis H37Rv MIC>90 = 24.1 ug ml-1 PMID[479022]
NPT18 Organism Pseudomonas aeruginosa Pseudomonas aeruginosa Inhibition = 7.0 % PMID[479022]
NPT20 Organism Candida albicans Candida albicans Inhibition = 17.0 % PMID[479022]
NPT20 Organism Candida albicans Candida albicans MIC>90 > 10.0 ug ml-1 PMID[479022]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus Inhibition = 86.0 % PMID[479022]
NPT19 Organism Escherichia coli Escherichia coli Inhibition = 17.0 % PMID[479022]
NPT747 Organism Acinetobacter baumannii Acinetobacter baumannii Inhibition = 37.0 % PMID[479022]
NPT747 Organism Acinetobacter baumannii Acinetobacter baumannii MIC>90 > 10.0 ug ml-1 PMID[479022]
NPT602 Organism Mycobacterium smegmatis Mycobacterium smegmatis Inhibition = 3.0 % PMID[479022]
NPT602 Organism Mycobacterium smegmatis Mycobacterium smegmatis MIC>90 > 10.0 ug ml-1 PMID[479022]
NPT88 Organism Mycobacterium tuberculosis Mycobacterium tuberculosis MIC>90 = 12.1 ug ml-1 PMID[479022]
NPT88 Organism Mycobacterium tuberculosis Mycobacterium tuberculosis MIC>90 = 20.6 ug ml-1 PMID[479022]
NPT88 Organism Mycobacterium tuberculosis Mycobacterium tuberculosis MIC>90 = 12.4 ug ml-1 PMID[479022]
NPT88 Organism Mycobacterium tuberculosis Mycobacterium tuberculosis MIC>90 = 9.0 ug ml-1 PMID[479022]
NPT88 Organism Mycobacterium tuberculosis Mycobacterium tuberculosis MIC>90 = 9.6 ug ml-1 PMID[479022]
NPT88 Organism Mycobacterium tuberculosis Mycobacterium tuberculosis MIC>90 = 11.6 ug ml-1 PMID[479022]
NPT88 Organism Mycobacterium tuberculosis Mycobacterium tuberculosis MIC>90 = 19.2 ug ml-1 PMID[479022]
NPT88 Organism Mycobacterium tuberculosis Mycobacterium tuberculosis MIC>90 = 9.3 ug ml-1 PMID[479022]
NPT88 Organism Mycobacterium tuberculosis Mycobacterium tuberculosis MIC>90 = 16.9 ug ml-1 PMID[479022]
NPT88 Organism Mycobacterium tuberculosis Mycobacterium tuberculosis MIC>90 = 22.9 ug ml-1 PMID[479022]
NPT88 Organism Mycobacterium tuberculosis Mycobacterium tuberculosis MIC>90 = 9.7 ug ml-1 PMID[479022]
NPT88 Organism Mycobacterium tuberculosis Mycobacterium tuberculosis MIC>90 = 2.4 ug ml-1 PMID[479022]
NPT790 Organism Mycobacterium tuberculosis H37Rv Mycobacterium tuberculosis H37Rv MIC>90 = 11.3 ug ml-1 PMID[479022]
NPT19 Organism Escherichia coli Escherichia coli MIC>90 > 10.0 ug ml-1 PMID[479022]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC>90 > 10.0 ug ml-1 PMID[479022]

☑ 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 NPC301010 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
0.9885 High Similarity NPC280066
0.7128 Intermediate Similarity NPC84128
0.7128 Intermediate Similarity NPC53858
0.6804 Remote Similarity NPC472351
0.6803 Remote Similarity NPC313657
0.6698 Remote Similarity NPC475188
0.6667 Remote Similarity NPC23984
0.663 Remote Similarity NPC266888
0.663 Remote Similarity NPC161774
0.663 Remote Similarity NPC256312
0.6559 Remote Similarity NPC327272
0.6458 Remote Similarity NPC31756
0.6452 Remote Similarity NPC209156
0.6413 Remote Similarity NPC196007
0.6413 Remote Similarity NPC214532
0.6413 Remote Similarity NPC76297
0.6396 Remote Similarity NPC128303
0.6392 Remote Similarity NPC476156
0.6392 Remote Similarity NPC476117
0.6392 Remote Similarity NPC476137
0.6392 Remote Similarity NPC476243
0.6364 Remote Similarity NPC235078
0.6339 Remote Similarity NPC241394
0.6327 Remote Similarity NPC476302
0.6289 Remote Similarity NPC312315
0.6263 Remote Similarity NPC284456
0.6263 Remote Similarity NPC6902
0.6263 Remote Similarity NPC184473
0.619 Remote Similarity NPC474576
0.6176 Remote Similarity NPC477539
0.6162 Remote Similarity NPC470783
0.6154 Remote Similarity NPC275715
0.6132 Remote Similarity NPC173763
0.6132 Remote Similarity NPC62263
0.6132 Remote Similarity NPC471098
0.6095 Remote Similarity NPC475801
0.6095 Remote Similarity NPC474593
0.6087 Remote Similarity NPC250953
0.6058 Remote Similarity NPC473495
0.6022 Remote Similarity NPC322274
0.602 Remote Similarity NPC191774
0.5888 Remote Similarity NPC477538
0.587 Remote Similarity NPC128005
0.587 Remote Similarity NPC84182
0.5854 Remote Similarity NPC477237
0.5849 Remote Similarity NPC155230
0.5825 Remote Similarity NPC124359
0.5818 Remote Similarity NPC117829
0.5804 Remote Similarity NPC220234
0.5778 Remote Similarity NPC314510
0.5773 Remote Similarity NPC320221
0.5766 Remote Similarity NPC47076
0.5766 Remote Similarity NPC473597
0.5766 Remote Similarity NPC134504
0.5761 Remote Similarity NPC262615
0.576 Remote Similarity NPC477238
0.573 Remote Similarity NPC327748
0.573 Remote Similarity NPC321468
0.5726 Remote Similarity NPC469899
0.5699 Remote Similarity NPC287693
0.5667 Remote Similarity NPC327170
0.5667 Remote Similarity NPC329564
0.5664 Remote Similarity NPC475440
0.5652 Remote Similarity NPC124554
0.5652 Remote Similarity NPC301148
0.5652 Remote Similarity NPC5864
0.5636 Remote Similarity NPC38172
0.5607 Remote Similarity NPC168017
0.5603 Remote Similarity NPC198344
0.56 Remote Similarity NPC59867

  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 NPC301010 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
0.701 Intermediate Similarity NPD7760 Phase 2
0.701 Intermediate Similarity NPD7759 Phase 2
0.6947 Remote Similarity NPD2683 Discontinued
0.6842 Remote Similarity NPD7762 Phase 2
0.6842 Remote Similarity NPD7763 Phase 2
0.6768 Remote Similarity NPD3176 Clinical (unspecified phase)
0.6698 Remote Similarity NPD4825 Clinical (unspecified phase)
0.6602 Remote Similarity NPD6699 Clinical (unspecified phase)
0.6415 Remote Similarity NPD7841 Clinical (unspecified phase)
0.6373 Remote Similarity NPD3177 Phase 3
0.6346 Remote Similarity NPD4261 Phase 1
0.6296 Remote Similarity NPD8038 Phase 2
0.6263 Remote Similarity NPD1125 Discovery
0.6087 Remote Similarity NPD322 Phase 1
0.6038 Remote Similarity NPD5792 Clinical (unspecified phase)
0.6038 Remote Similarity NPD2682 Approved
0.6036 Remote Similarity NPD6120 Clinical (unspecified phase)
0.6022 Remote Similarity NPD620 Approved
0.602 Remote Similarity NPD4278 Clinical (unspecified phase)
0.6019 Remote Similarity NPD3723 Clinical (unspecified phase)
0.6018 Remote Similarity NPD6122 Discontinued
0.5856 Remote Similarity NPD3714 Approved
0.5856 Remote Similarity NPD3713 Approved
0.5856 Remote Similarity NPD3715 Approved
0.5825 Remote Similarity NPD3733 Clinical (unspecified phase)
0.5761 Remote Similarity NPD6438 Approved
0.5761 Remote Similarity NPD6437 Approved
0.5755 Remote Similarity NPD868 Phase 3
0.5755 Remote Similarity NPD867 Phase 3
0.5729 Remote Similarity NPD5386 Phase 2
0.5726 Remote Similarity NPD6937 Approved
0.5714 Remote Similarity NPD5791 Phase 2
0.5644 Remote Similarity NPD4815 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