Structure

Physi-Chem Properties

Molecular Weight:  466.28
Volume:  478.717
LogP:  0.042
LogD:  -0.015
LogS:  -0.903
# Rotatable Bonds:  9
TPSA:  136.45
# H-Bond Aceptor:  10
# H-Bond Donor:  2
# Rings:  1
# Heavy Atoms:  10

MedChem Properties

QED Drug-Likeness Score:  0.408
Synthetic Accessibility Score:  4.508
Fsp3:  0.739
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.847
MDCK Permeability:  5.904926365474239e-05
Pgp-inhibitor:  0.97
Pgp-substrate:  0.349
Human Intestinal Absorption (HIA):  0.773
20% Bioavailability (F20%):  0.022
30% Bioavailability (F30%):  0.968

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.607
Plasma Protein Binding (PPB):  34.013877868652344%
Volume Distribution (VD):  0.529
Pgp-substrate:  74.7868423461914%

ADMET: Metabolism

CYP1A2-inhibitor:  0.003
CYP1A2-substrate:  0.04
CYP2C19-inhibitor:  0.029
CYP2C19-substrate:  0.063
CYP2C9-inhibitor:  0.014
CYP2C9-substrate:  0.195
CYP2D6-inhibitor:  0.054
CYP2D6-substrate:  0.12
CYP3A4-inhibitor:  0.016
CYP3A4-substrate:  0.173

ADMET: Excretion

Clearance (CL):  5.561
Half-life (T1/2):  0.594

ADMET: Toxicity

hERG Blockers:  0.004
Human Hepatotoxicity (H-HT):  0.661
Drug-inuced Liver Injury (DILI):  0.943
AMES Toxicity:  0.011
Rat Oral Acute Toxicity:  0.013
Maximum Recommended Daily Dose:  0.048
Skin Sensitization:  0.729
Carcinogencity:  0.02
Eye Corrosion:  0.007
Eye Irritation:  0.019
Respiratory Toxicity:  0.905

Download Data

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

  Natural Product: NPC469739

Natural Product ID:  NPC469739
Common Name*:   Sclerotiotide I
IUPAC Name:   (2E,4E,6R,7R)-6,7-dihydroxy-N-[(3S,6S,9S)-3,4,7-trimethyl-2,5,8-trioxo-6-propan-2-yl-1,4,7-triazacyclododec-9-yl]octa-2,4-dienamide
Synonyms:   sclerotiotide I
Standard InCHIKey:  DMCVGIKLKNPCAA-JNPMBWLGSA-N
Standard InCHI:  InChI=1S/C23H38N4O6/c1-14(2)20-23(33)26(5)15(3)21(31)24-13-9-10-17(22(32)27(20)6)25-19(30)12-8-7-11-18(29)16(4)28/h7-8,11-12,14-18,20,28-29H,9-10,13H2,1-6H3,(H,24,31)(H,25,30)/b11-7+,12-8+/t15-,16+,17-,18+,20-/m0/s1
SMILES:  C[C@H]([C@@H](/C=C/C=C/C(=N[C@H]1CCCN=C(O)[C@@H](N(C(=O)[C@@H](N(C1=O)C)C(C)C)C)C)O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1164866
PubChem CID:   46906559
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
NPO33363 aspergillus sclerotiorum pt06-1 Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[20503985]

☑ 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
NPT20 Organism Candida albicans Candida albicans MIC = 6700.0 nM PMID[509822]

☑ 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 NPC469739 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
0.8523 High Similarity NPC284456
0.8315 Intermediate Similarity NPC6902
0.828 Intermediate Similarity NPC155230
0.7912 Intermediate Similarity NPC184473
0.75 Intermediate Similarity NPC251122
0.7387 Intermediate Similarity NPC103391
0.7387 Intermediate Similarity NPC472536
0.7103 Intermediate Similarity NPC476877
0.7009 Intermediate Similarity NPC471097
0.7009 Intermediate Similarity NPC475149
0.6981 Remote Similarity NPC13175
0.6981 Remote Similarity NPC475791
0.6972 Remote Similarity NPC476876
0.6893 Remote Similarity NPC38172
0.6887 Remote Similarity NPC475758
0.6881 Remote Similarity NPC205176
0.6864 Remote Similarity NPC315188
0.6807 Remote Similarity NPC273185
0.6742 Remote Similarity NPC315141
0.6742 Remote Similarity NPC129995
0.6696 Remote Similarity NPC171734
0.6696 Remote Similarity NPC207820
0.6667 Remote Similarity NPC476875
0.6606 Remote Similarity NPC188785
0.6517 Remote Similarity NPC253468
0.6517 Remote Similarity NPC235311
0.6489 Remote Similarity NPC314678
0.6466 Remote Similarity NPC314550
0.6441 Remote Similarity NPC296043
0.6436 Remote Similarity NPC475975
0.6408 Remote Similarity NPC473495
0.6404 Remote Similarity NPC474099
0.6396 Remote Similarity NPC474244
0.6387 Remote Similarity NPC329216
0.6346 Remote Similarity NPC320057
0.632 Remote Similarity NPC473249
0.6311 Remote Similarity NPC160688
0.629 Remote Similarity NPC36254
0.6281 Remote Similarity NPC470788
0.6277 Remote Similarity NPC97614
0.625 Remote Similarity NPC201244
0.625 Remote Similarity NPC477217
0.623 Remote Similarity NPC470652
0.6222 Remote Similarity NPC471023
0.6222 Remote Similarity NPC477106
0.6218 Remote Similarity NPC272166
0.6198 Remote Similarity NPC476155
0.6198 Remote Similarity NPC17581
0.6198 Remote Similarity NPC239357
0.6176 Remote Similarity NPC228638
0.6172 Remote Similarity NPC319766
0.617 Remote Similarity NPC471022
0.6167 Remote Similarity NPC66007
0.6165 Remote Similarity NPC127741
0.6162 Remote Similarity NPC31756
0.616 Remote Similarity NPC470654
0.616 Remote Similarity NPC470650
0.616 Remote Similarity NPC470653
0.6159 Remote Similarity NPC135121
0.6139 Remote Similarity NPC226982
0.6139 Remote Similarity NPC277341
0.6124 Remote Similarity NPC469666
0.6111 Remote Similarity NPC6975
0.61 Remote Similarity NPC476137
0.61 Remote Similarity NPC476117
0.61 Remote Similarity NPC476156
0.61 Remote Similarity NPC476243
0.6095 Remote Similarity NPC324506
0.6087 Remote Similarity NPC477525
0.608 Remote Similarity NPC50520
0.6075 Remote Similarity NPC474576
0.6074 Remote Similarity NPC476259
0.6071 Remote Similarity NPC26597
0.6071 Remote Similarity NPC233932
0.6066 Remote Similarity NPC470300
0.6058 Remote Similarity NPC52748
0.6053 Remote Similarity NPC474827
0.6053 Remote Similarity NPC199831
0.6053 Remote Similarity NPC68001
0.6053 Remote Similarity NPC474828
0.6045 Remote Similarity NPC68865
0.604 Remote Similarity NPC476302
0.604 Remote Similarity NPC470783
0.6038 Remote Similarity NPC316186
0.6036 Remote Similarity NPC52820
0.6032 Remote Similarity NPC97580
0.6032 Remote Similarity NPC252878
0.6031 Remote Similarity NPC130309
0.6019 Remote Similarity NPC471098
0.6019 Remote Similarity NPC173763
0.6019 Remote Similarity NPC62263
0.6016 Remote Similarity NPC470545
0.6014 Remote Similarity NPC315266
0.6 Remote Similarity NPC315210
0.6 Remote Similarity NPC74035
0.6 Remote Similarity NPC315848
0.6 Remote Similarity NPC6795
0.5984 Remote Similarity NPC46427
0.5981 Remote Similarity NPC474593
0.5981 Remote Similarity NPC475801
0.598 Remote Similarity NPC53858
0.598 Remote Similarity NPC246005
0.598 Remote Similarity NPC84128
0.5971 Remote Similarity NPC314358
0.5968 Remote Similarity NPC470546
0.5956 Remote Similarity NPC163392
0.5956 Remote Similarity NPC307357
0.5956 Remote Similarity NPC268841
0.5956 Remote Similarity NPC46098
0.5956 Remote Similarity NPC239762
0.5952 Remote Similarity NPC202521
0.5946 Remote Similarity NPC175614
0.5946 Remote Similarity NPC473597
0.5935 Remote Similarity NPC470544
0.5922 Remote Similarity NPC235078
0.5918 Remote Similarity NPC288086
0.5913 Remote Similarity NPC55336
0.5912 Remote Similarity NPC168113
0.5899 Remote Similarity NPC313867
0.5899 Remote Similarity NPC316008
0.5891 Remote Similarity NPC470655
0.5891 Remote Similarity NPC470651
0.5887 Remote Similarity NPC471821
0.5887 Remote Similarity NPC471820
0.5882 Remote Similarity NPC23984
0.5878 Remote Similarity NPC120335
0.5873 Remote Similarity NPC476990
0.5873 Remote Similarity NPC200964
0.587 Remote Similarity NPC197682
0.587 Remote Similarity NPC176226
0.5865 Remote Similarity NPC472351
0.5865 Remote Similarity NPC246079
0.5857 Remote Similarity NPC262077
0.5851 Remote Similarity NPC187315
0.5845 Remote Similarity NPC2501
0.5842 Remote Similarity NPC312315
0.5841 Remote Similarity NPC220234
0.5833 Remote Similarity NPC473341
0.5833 Remote Similarity NPC262166
0.5827 Remote Similarity NPC315283
0.5827 Remote Similarity NPC314388
0.5825 Remote Similarity NPC82799
0.5821 Remote Similarity NPC287401
0.581 Remote Similarity NPC477199
0.581 Remote Similarity NPC470943
0.58 Remote Similarity NPC63931
0.5798 Remote Similarity NPC133729
0.5798 Remote Similarity NPC298484
0.5797 Remote Similarity NPC269398
0.5797 Remote Similarity NPC263493
0.5795 Remote Similarity NPC471992
0.5784 Remote Similarity NPC157173
0.5772 Remote Similarity NPC473819
0.5769 Remote Similarity NPC101719
0.5766 Remote Similarity NPC476133
0.5766 Remote Similarity NPC178662
0.5766 Remote Similarity NPC470884
0.5766 Remote Similarity NPC92784
0.5766 Remote Similarity NPC98424
0.5766 Remote Similarity NPC313265
0.5763 Remote Similarity NPC315426
0.5761 Remote Similarity NPC29468
0.5758 Remote Similarity NPC473322
0.5755 Remote Similarity NPC161069
0.5755 Remote Similarity NPC477539
0.5753 Remote Similarity NPC476268
0.575 Remote Similarity NPC469603
0.5739 Remote Similarity NPC77703
0.5739 Remote Similarity NPC313234
0.5736 Remote Similarity NPC313173
0.5733 Remote Similarity NPC471051
0.5733 Remote Similarity NPC471052
0.5733 Remote Similarity NPC471053
0.5728 Remote Similarity NPC209232
0.5726 Remote Similarity NPC128303
0.5726 Remote Similarity NPC469604
0.5724 Remote Similarity NPC122590
0.5714 Remote Similarity NPC50902
0.5714 Remote Similarity NPC189764
0.5714 Remote Similarity NPC476276
0.5714 Remote Similarity NPC233273
0.5714 Remote Similarity NPC205546
0.5704 Remote Similarity NPC477400
0.5704 Remote Similarity NPC329761
0.5704 Remote Similarity NPC145113
0.5704 Remote Similarity NPC225648
0.5703 Remote Similarity NPC66855
0.5703 Remote Similarity NPC71684
0.5702 Remote Similarity NPC170375
0.5702 Remote Similarity NPC475440
0.57 Remote Similarity NPC217095
0.57 Remote Similarity NPC264417
0.5694 Remote Similarity NPC475168
0.5694 Remote Similarity NPC7817
0.5693 Remote Similarity NPC471264
0.5693 Remote Similarity NPC471265
0.5692 Remote Similarity NPC247902
0.5692 Remote Similarity NPC222466
0.5692 Remote Similarity NPC262880
0.569 Remote Similarity NPC124554

  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 NPC469739 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
0.632 Remote Similarity NPD7747 Phase 1
0.632 Remote Similarity NPD7746 Phase 1
0.6218 Remote Similarity NPD1000 Clinical (unspecified phase)
0.62 Remote Similarity NPD7762 Phase 2
0.62 Remote Similarity NPD7763 Phase 2
0.6075 Remote Similarity NPD6095 Approved
0.6075 Remote Similarity NPD6094 Approved
0.6 Remote Similarity NPD7623 Phase 3
0.6 Remote Similarity NPD7624 Clinical (unspecified phase)
0.6 Remote Similarity NPD3626 Phase 3
0.5943 Remote Similarity NPD3177 Phase 3
0.5897 Remote Similarity NPD2147 Approved
0.5882 Remote Similarity NPD6421 Discontinued
0.5859 Remote Similarity NPD8273 Phase 1
0.5856 Remote Similarity NPD7841 Clinical (unspecified phase)
0.582 Remote Similarity NPD2100 Approved
0.5806 Remote Similarity NPD2099 Approved
0.5794 Remote Similarity NPD7739 Clinical (unspecified phase)
0.5785 Remote Similarity NPD2090 Approved
0.5755 Remote Similarity NPD3723 Clinical (unspecified phase)
0.5714 Remote Similarity NPD7979 Clinical (unspecified phase)
0.5702 Remote Similarity NPD7116 Clinical (unspecified phase)
0.5702 Remote Similarity NPD7601 Clinical (unspecified phase)
0.5693 Remote Similarity NPD8173 Phase 2
0.5693 Remote Similarity NPD8172 Phase 2
0.568 Remote Similarity NPD3123 Discovery
0.5676 Remote Similarity NPD7118 Clinical (unspecified phase)
0.5673 Remote Similarity NPD2683 Discontinued
0.5664 Remote Similarity NPD4228 Discovery
0.5649 Remote Similarity NPD3125 Approved
0.5636 Remote Similarity NPD4261 Phase 1
0.562 Remote Similarity NPD7113 Clinical (unspecified phase)
0.562 Remote Similarity NPD5767 Discontinued
0.5607 Remote Similarity NPD7759 Phase 2
0.5607 Remote Similarity NPD7760 Phase 2
0.5603 Remote Similarity NPD6681 Discovery

  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