Structure

Physi-Chem Properties

Molecular Weight:  473.95
Volume:  344.223
LogP:  1.447
LogD:  1.644
LogS:  -2.781
# Rotatable Bonds:  6
TPSA:  108.83
# H-Bond Aceptor:  8
# H-Bond Donor:  3
# Rings:  3
# Heavy Atoms:  10

MedChem Properties

QED Drug-Likeness Score:  0.597
Synthetic Accessibility Score:  4.75
Fsp3:  0.4
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.298
MDCK Permeability:  1.7244381524506025e-05
Pgp-inhibitor:  0.991
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.726
20% Bioavailability (F20%):  0.968
30% Bioavailability (F30%):  0.997

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.906
Plasma Protein Binding (PPB):  75.06900787353516%
Volume Distribution (VD):  1.326
Pgp-substrate:  37.24826431274414%

ADMET: Metabolism

CYP1A2-inhibitor:  0.534
CYP1A2-substrate:  0.137
CYP2C19-inhibitor:  0.837
CYP2C19-substrate:  0.239
CYP2C9-inhibitor:  0.238
CYP2C9-substrate:  0.08
CYP2D6-inhibitor:  0.523
CYP2D6-substrate:  0.022
CYP3A4-inhibitor:  0.902
CYP3A4-substrate:  0.298

ADMET: Excretion

Clearance (CL):  1.946
Half-life (T1/2):  0.863

ADMET: Toxicity

hERG Blockers:  0.081
Human Hepatotoxicity (H-HT):  0.915
Drug-inuced Liver Injury (DILI):  0.924
AMES Toxicity:  0.948
Rat Oral Acute Toxicity:  0.991
Maximum Recommended Daily Dose:  0.938
Skin Sensitization:  0.924
Carcinogencity:  0.035
Eye Corrosion:  0.003
Eye Irritation:  0.011
Respiratory Toxicity:  0.972

Download Data

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

  Natural Product: NPC201900

Natural Product ID:  NPC201900
Common Name*:   Aerophobin 1
IUPAC Name:   (5R,6S)-7,9-dibromo-6-hydroxy-N-[2-(1H-imidazol-5-yl)ethyl]-8-methoxy-1-oxa-2-azaspiro[4.5]deca-2,7,9-triene-3-carboxamide
Synonyms:   Aerophobin 1
Standard InCHIKey:  MDUQIEXQKMPARD-HIFRSBDPSA-N
Standard InCHI:  InChI=1S/C15H16Br2N4O4/c1-24-12-9(16)4-15(13(22)11(12)17)5-10(21-25-15)14(23)19-3-2-8-6-18-7-20-8/h4,6-7,13,22H,2-3,5H2,1H3,(H,18,20)(H,19,23)/t13-,15+/m1/s1
SMILES:  COC1=C([C@H]([C@]2(C=C1Br)CC(=NO2)C(=O)NCCc1cnc[nH]1)O)Br
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL499178
PubChem CID:   14484009
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0002490] Azolines
        • [CHEMONTID:0002211] Isoxazolines

*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
NPO33394 druinella sp. Species n.a. n.a. n.a. Fujian, China n.a. PMID[12502317]
NPO13261 Suberea clavata Species Aplysinellidae Eukaryota n.a. Australian n.a. PMID[19379003]
NPO13261 Suberea clavata Species Aplysinellidae Eukaryota 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
NPT179 Cell Line A2780 Homo sapiens ID50 = 21.53 ug ml-1 PMID[515687]
NPT111 Cell Line K562 Homo sapiens ID50 = 24.11 ug ml-1 PMID[515687]
NPT4197 Individual Protein Coagulation factor XI Homo sapiens Inhibition = 59.0 % PMID[515688]
NPT4655 Individual Protein Coagulation factor IX Homo sapiens Inhibition < 5.0 % PMID[515688]

☑ 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 NPC201900 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
0.7209 Intermediate Similarity NPC304257
0.711 Intermediate Similarity NPC181086
0.7029 Intermediate Similarity NPC81079
0.6902 Remote Similarity NPC60537
0.6869 Remote Similarity NPC477118
0.6834 Remote Similarity NPC477120
0.6824 Remote Similarity NPC145149
0.6784 Remote Similarity NPC260270
0.6735 Remote Similarity NPC477119
0.6685 Remote Similarity NPC174020
0.6606 Remote Similarity NPC238945
0.6556 Remote Similarity NPC286696
0.6467 Remote Similarity NPC327477
0.6464 Remote Similarity NPC185903
0.6437 Remote Similarity NPC180462
0.6406 Remote Similarity NPC113369
0.6389 Remote Similarity NPC237812
0.6389 Remote Similarity NPC18223
0.6384 Remote Similarity NPC235501
0.6384 Remote Similarity NPC25465
0.6344 Remote Similarity NPC323244
0.6304 Remote Similarity NPC328924
0.6264 Remote Similarity NPC66855
0.6245 Remote Similarity NPC156003
0.6244 Remote Similarity NPC282247
0.623 Remote Similarity NPC210947
0.6217 Remote Similarity NPC179896
0.6215 Remote Similarity NPC1702
0.6215 Remote Similarity NPC158672
0.6196 Remote Similarity NPC289324
0.6193 Remote Similarity NPC313173
0.619 Remote Similarity NPC313504
0.6178 Remote Similarity NPC282531
0.6154 Remote Similarity NPC242923
0.6154 Remote Similarity NPC133782
0.6154 Remote Similarity NPC144474
0.6154 Remote Similarity NPC527
0.6135 Remote Similarity NPC101676
0.6111 Remote Similarity NPC54537
0.6111 Remote Similarity NPC477220
0.6099 Remote Similarity NPC126634
0.6091 Remote Similarity NPC476524
0.6091 Remote Similarity NPC476525
0.6062 Remote Similarity NPC469717
0.6054 Remote Similarity NPC470139
0.6043 Remote Similarity NPC8590
0.6023 Remote Similarity NPC327613
0.6 Remote Similarity NPC313514
0.599 Remote Similarity NPC124276
0.5978 Remote Similarity NPC470140
0.5957 Remote Similarity NPC74306
0.5957 Remote Similarity NPC315642
0.5955 Remote Similarity NPC15566
0.592 Remote Similarity NPC41333
0.5895 Remote Similarity NPC308906
0.589 Remote Similarity NPC89987
0.5882 Remote Similarity NPC89562
0.588 Remote Similarity NPC300139
0.588 Remote Similarity NPC233431
0.5872 Remote Similarity NPC69843
0.5867 Remote Similarity NPC54981
0.5853 Remote Similarity NPC475286
0.5853 Remote Similarity NPC174281
0.5853 Remote Similarity NPC477634
0.582 Remote Similarity NPC202166
0.582 Remote Similarity NPC473261
0.582 Remote Similarity NPC473262
0.582 Remote Similarity NPC300912
0.5808 Remote Similarity NPC12100
0.5799 Remote Similarity NPC136957
0.5799 Remote Similarity NPC19696
0.5796 Remote Similarity NPC320968
0.5796 Remote Similarity NPC477417
0.5796 Remote Similarity NPC477419
0.5792 Remote Similarity NPC243319
0.5789 Remote Similarity NPC470886
0.5765 Remote Similarity NPC473646
0.5761 Remote Similarity NPC470138
0.5755 Remote Similarity NPC265111
0.5746 Remote Similarity NPC54744
0.5733 Remote Similarity NPC71238
0.5714 Remote Similarity NPC475736
0.5714 Remote Similarity NPC314491
0.5708 Remote Similarity NPC17305
0.5697 Remote Similarity NPC171393
0.5697 Remote Similarity NPC295452
0.5688 Remote Similarity NPC280638
0.5665 Remote Similarity NPC474195
0.5662 Remote Similarity NPC476526
0.5662 Remote Similarity NPC329765
0.5662 Remote Similarity NPC48117
0.566 Remote Similarity NPC64216
0.5652 Remote Similarity NPC54214
0.5641 Remote Similarity NPC130714
0.5636 Remote Similarity NPC474196
0.5619 Remote Similarity NPC197068
0.5618 Remote Similarity NPC477633
0.5614 Remote Similarity NPC155498
0.5606 Remote Similarity NPC321052
0.5605 Remote Similarity NPC9635
0.5605 Remote Similarity NPC300183
0.56 Remote Similarity NPC473376

  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 NPC201900 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
0.7043 Intermediate Similarity NPD3130 Discontinued
0.6963 Remote Similarity NPD3105 Discontinued
0.6919 Remote Similarity NPD2604 Approved
0.6902 Remote Similarity NPD2180 Approved
0.6828 Remote Similarity NPD3697 Discontinued
0.676 Remote Similarity NPD1451 Approved
0.6682 Remote Similarity NPD8271 Discontinued
0.6667 Remote Similarity NPD1731 Clinical (unspecified phase)
0.6597 Remote Similarity NPD5768 Phase 2
0.6503 Remote Similarity NPD9627 Approved
0.6484 Remote Similarity NPD9183 Clinical (unspecified phase)
0.6465 Remote Similarity NPD3108 Clinical (unspecified phase)
0.6464 Remote Similarity NPD875 Clinical (unspecified phase)
0.6455 Remote Similarity NPD7980 Clinical (unspecified phase)
0.6448 Remote Similarity NPD3706 Clinical (unspecified phase)
0.6447 Remote Similarity NPD8119 Discontinued
0.6437 Remote Similarity NPD300 Approved
0.6389 Remote Similarity NPD9133 Approved
0.6359 Remote Similarity NPD5342 Clinical (unspecified phase)
0.6344 Remote Similarity NPD8292 Phase 2
0.633 Remote Similarity NPD7465 Suspended
0.63 Remote Similarity NPD8075 Discontinued
0.6298 Remote Similarity NPD9628 Approved
0.6209 Remote Similarity NPD8641 Approved
0.6183 Remote Similarity NPD566 Approved
0.6183 Remote Similarity NPD567 Approved
0.6183 Remote Similarity NPD568 Approved
0.6121 Remote Similarity NPD1249 Clinical (unspecified phase)
0.6119 Remote Similarity NPD7834 Approved
0.6111 Remote Similarity NPD8629 Discontinued
0.6106 Remote Similarity NPD8105 Discontinued
0.6091 Remote Similarity NPD7981 Discontinued
0.6081 Remote Similarity NPD949 Phase 1
0.6066 Remote Similarity NPD459 Clinical (unspecified phase)
0.6045 Remote Similarity NPD8410 Clinical (unspecified phase)
0.604 Remote Similarity NPD3347 Clinical (unspecified phase)
0.6036 Remote Similarity NPD8261 Discontinued
0.601 Remote Similarity NPD536 Clinical (unspecified phase)
0.6 Remote Similarity NPD7138 Phase 2
0.5991 Remote Similarity NPD6545 Clinical (unspecified phase)
0.5981 Remote Similarity NPD978 Clinical (unspecified phase)
0.5972 Remote Similarity NPD2152 Clinical (unspecified phase)
0.5957 Remote Similarity NPD582 Approved
0.5957 Remote Similarity NPD1117 Clinical (unspecified phase)
0.5923 Remote Similarity NPD6164 Phase 2
0.5923 Remote Similarity NPD6165 Phase 2
0.5907 Remote Similarity NPD8113 Phase 2
0.5905 Remote Similarity NPD7245 Approved
0.5905 Remote Similarity NPD7246 Clinical (unspecified phase)
0.5826 Remote Similarity NPD534 Phase 2
0.5826 Remote Similarity NPD4555 Clinical (unspecified phase)
0.5826 Remote Similarity NPD537 Phase 2
0.5808 Remote Similarity NPD2812 Clinical (unspecified phase)
0.5808 Remote Similarity NPD2813 Phase 3
0.5803 Remote Similarity NPD775 Approved
0.5801 Remote Similarity NPD245 Suspended
0.5792 Remote Similarity NPD3497 Clinical (unspecified phase)
0.5792 Remote Similarity NPD9081 Clinical (unspecified phase)
0.5778 Remote Similarity NPD1389 Clinical (unspecified phase)
0.5778 Remote Similarity NPD1388 Phase 1
0.5778 Remote Similarity NPD1390 Phase 1
0.5775 Remote Similarity NPD2009 Clinical (unspecified phase)
0.5767 Remote Similarity NPD1118 Discontinued
0.5759 Remote Similarity NPD796 Phase 2
0.5741 Remote Similarity NPD996 Phase 2
0.5741 Remote Similarity NPD994 Phase 2
0.574 Remote Similarity NPD1915 Phase 1
0.5738 Remote Similarity NPD1807 Clinical (unspecified phase)
0.5733 Remote Similarity NPD4612 Discontinued
0.5732 Remote Similarity NPD7415 Suspended
0.5729 Remote Similarity NPD3405 Phase 3
0.572 Remote Similarity NPD8442 Discontinued
0.5687 Remote Similarity NPD1783 Clinical (unspecified phase)
0.5684 Remote Similarity NPD6036 Suspended
0.5683 Remote Similarity NPD5072 Discontinued
0.5682 Remote Similarity NPD9132 Discontinued
0.5676 Remote Similarity NPD7689 Approved
0.5671 Remote Similarity NPD8257 Approved
0.5671 Remote Similarity NPD8258 Clinical (unspecified phase)
0.5671 Remote Similarity NPD8256 Approved
0.5657 Remote Similarity NPD1030 Approved
0.5657 Remote Similarity NPD1027 Approved
0.5657 Remote Similarity NPD1029 Clinical (unspecified phase)
0.5656 Remote Similarity NPD5665 Clinical (unspecified phase)
0.5654 Remote Similarity NPD2253 Discontinued
0.5644 Remote Similarity NPD516 Clinical (unspecified phase)
0.5636 Remote Similarity NPD3042 Approved
0.5636 Remote Similarity NPD3043 Approved
0.5634 Remote Similarity NPD1096 Discontinued
0.5633 Remote Similarity NPD8458 Clinical (unspecified phase)
0.5609 Remote Similarity NPD8488 Clinical (unspecified phase)
0.5605 Remote Similarity NPD8250 Phase 2
0.5603 Remote Similarity NPD7471 Discontinued
0.5602 Remote Similarity NPD549 Approved
0.56 Remote Similarity NPD8169 Discontinued
0.56 Remote Similarity NPD1303 Phase 1

  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