Structure

Physi-Chem Properties

Molecular Weight:  563.33
Volume:  573.791
LogP:  1.081
LogD:  0.994
LogS:  -2.201
# Rotatable Bonds:  4
TPSA:  145.43
# H-Bond Aceptor:  12
# H-Bond Donor:  2
# Rings:  2
# Heavy Atoms:  12

MedChem Properties

QED Drug-Likeness Score:  0.373
Synthetic Accessibility Score:  4.986
Fsp3:  0.714
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:  -5.393
MDCK Permeability:  1.935995533131063e-05
Pgp-inhibitor:  0.674
Pgp-substrate:  0.701
Human Intestinal Absorption (HIA):  0.915
20% Bioavailability (F20%):  0.011
30% Bioavailability (F30%):  0.778

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.336
Plasma Protein Binding (PPB):  50.03997039794922%
Volume Distribution (VD):  0.405
Pgp-substrate:  50.469993591308594%

ADMET: Metabolism

CYP1A2-inhibitor:  0.001
CYP1A2-substrate:  0.044
CYP2C19-inhibitor:  0.033
CYP2C19-substrate:  0.188
CYP2C9-inhibitor:  0.032
CYP2C9-substrate:  0.126
CYP2D6-inhibitor:  0.009
CYP2D6-substrate:  0.114
CYP3A4-inhibitor:  0.566
CYP3A4-substrate:  0.655

ADMET: Excretion

Clearance (CL):  5.015
Half-life (T1/2):  0.843

ADMET: Toxicity

hERG Blockers:  0.002
Human Hepatotoxicity (H-HT):  0.774
Drug-inuced Liver Injury (DILI):  0.942
AMES Toxicity:  0.008
Rat Oral Acute Toxicity:  0.2
Maximum Recommended Daily Dose:  0.166
Skin Sensitization:  0.061
Carcinogencity:  0.01
Eye Corrosion:  0.003
Eye Irritation:  0.005
Respiratory Toxicity:  0.034

Download Data

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

  Natural Product: NPC13175

Natural Product ID:  NPC13175
Common Name*:   Destruxin A
IUPAC Name:   (3R,10S,13S,16S,19S)-10,11,14-trimethyl-13,16-di(propan-2-yl)-3-prop-2-enyl-4-oxa-1,8,11,14,17-pentazabicyclo[17.3.0]docosane-2,5,9,12,15,18-hexone
Synonyms:  
Standard InCHIKey:  QRPSKGICZOQNNG-GDXKHXNESA-N
Standard InCHI:  InChI=1S/C28H45N5O7/c1-9-11-20-26(37)33-15-10-12-19(33)25(36)30-22(16(2)3)27(38)32(8)23(17(4)5)28(39)31(7)18(6)24(35)29-14-13-21(34)40-20/h9,16-20,22-23H,1,10-15H2,2-8H3,(H,29,35)(H,30,36)/t18-,19-,20+,22-,23-/m0/s1
SMILES:  C=CC[C@@H]1C(=O)N2CCC[C@H]2C(=N[C@@H](C(C)C)C(=O)N(C)[C@@H](C(C)C)C(=O)N(C)[C@@H](C)C(=NCCC(=O)O1)O)O
Synthetic Gene Cluster:   BGC0000337;
ChEMBL Identifier:   CHEMBL474266
PubChem CID:   157382
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0001813] Peptidomimetics
        • [CHEMONTID:0001961] Depsipeptides
          • [CHEMONTID:0001994] Cyclic depsipeptides

*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
NPO9967 Metarhizium anisopliae Species Clavicipitaceae Eukaryota n.a. n.a. n.a. PMID[10650095]
NPO9967 Metarhizium anisopliae Species Clavicipitaceae Eukaryota n.a. n.a. n.a. PMID[18044842]
NPO9967 Metarhizium anisopliae Species Clavicipitaceae Eukaryota n.a. n.a. n.a. PMID[20233596]
NPO20842 Beauveria felina Species Cordycipitaceae Eukaryota n.a. n.a. n.a. PMID[21438588]
NPO20842 Beauveria felina Species Cordycipitaceae Eukaryota n.a. n.a. n.a. PMID[23822585]
NPO20842 Beauveria felina Species Cordycipitaceae Eukaryota n.a. n.a. n.a. PMID[26295595]
NPO24414 Trichoderma harzianum Species Hypocreaceae Eukaryota n.a. n.a. n.a. PMID[33301677]
NPO9967 Metarhizium anisopliae Species Clavicipitaceae Eukaryota n.a. n.a. n.a. PMID[7623030]
NPO24414 Trichoderma harzianum Species Hypocreaceae Eukaryota n.a. n.a. n.a. PMID[8201317]
NPO24414 Trichoderma harzianum Species Hypocreaceae Eukaryota n.a. n.a. n.a. PMID[8968392]
NPO20842 Beauveria felina Species Cordycipitaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9967 Metarhizium anisopliae Species Clavicipitaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24414 Trichoderma harzianum Species Hypocreaceae 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
NPT168 Cell Line P388 Mus musculus IC50 = 12500.0 nM PMID[558410]
NPT81 Cell Line A549 Homo sapiens IC50 = 13100.0 nM PMID[558410]
NPT139 Cell Line HT-29 Homo sapiens IC50 = 9300.0 nM PMID[558410]
NPT963 Organism Hepatitis B virus Hepatitis B virus IC50 = 0.1 ug/ml PMID[10479314]

☑ 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 NPC13175 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
1.0 High Similarity NPC475791
0.9891 High Similarity NPC475758
0.9787 High Similarity NPC471097
0.9787 High Similarity NPC475149
0.8723 High Similarity NPC474576
0.8632 High Similarity NPC173763
0.8632 High Similarity NPC62263
0.8632 High Similarity NPC471098
0.8617 High Similarity NPC475801
0.8617 High Similarity NPC474593
0.8365 Intermediate Similarity NPC171734
0.8119 Intermediate Similarity NPC475440
0.7798 Intermediate Similarity NPC476875
0.7664 Intermediate Similarity NPC475637
0.7477 Intermediate Similarity NPC476877
0.7429 Intermediate Similarity NPC220234
0.7407 Intermediate Similarity NPC323720
0.7339 Intermediate Similarity NPC476876
0.7238 Intermediate Similarity NPC473597
0.7222 Intermediate Similarity NPC301148
0.7222 Intermediate Similarity NPC124554
0.7222 Intermediate Similarity NPC5864
0.7156 Intermediate Similarity NPC198344
0.713 Intermediate Similarity NPC188785
0.7091 Intermediate Similarity NPC124549
0.7087 Intermediate Similarity NPC477538
0.7059 Intermediate Similarity NPC315188
0.7054 Intermediate Similarity NPC476133
0.7054 Intermediate Similarity NPC92784
0.7054 Intermediate Similarity NPC178662
0.7054 Intermediate Similarity NPC98424
0.7054 Intermediate Similarity NPC470884
0.7041 Intermediate Similarity NPC246005
0.6983 Remote Similarity NPC472536
0.6983 Remote Similarity NPC103391
0.6981 Remote Similarity NPC469739
0.6977 Remote Similarity NPC471265
0.6977 Remote Similarity NPC471264
0.6907 Remote Similarity NPC31756
0.6903 Remote Similarity NPC67009
0.6869 Remote Similarity NPC184473
0.6837 Remote Similarity NPC476243
0.6837 Remote Similarity NPC476156
0.6837 Remote Similarity NPC476137
0.6837 Remote Similarity NPC476117
0.6791 Remote Similarity NPC209509
0.6786 Remote Similarity NPC205176
0.6768 Remote Similarity NPC476302
0.6768 Remote Similarity NPC470783
0.6762 Remote Similarity NPC476019
0.6754 Remote Similarity NPC207820
0.6692 Remote Similarity NPC269398
0.6692 Remote Similarity NPC263493
0.6642 Remote Similarity NPC240848
0.6636 Remote Similarity NPC38172
0.66 Remote Similarity NPC475542
0.6585 Remote Similarity NPC273185
0.6562 Remote Similarity NPC263281
0.6562 Remote Similarity NPC178919
0.656 Remote Similarity NPC309525
0.6559 Remote Similarity NPC10716
0.6544 Remote Similarity NPC5620
0.6535 Remote Similarity NPC6902
0.6535 Remote Similarity NPC284456
0.6526 Remote Similarity NPC196007
0.6526 Remote Similarity NPC214532
0.6526 Remote Similarity NPC76297
0.6496 Remote Similarity NPC251122
0.6489 Remote Similarity NPC212866
0.6489 Remote Similarity NPC29598
0.6471 Remote Similarity NPC471202
0.6471 Remote Similarity NPC63191
0.6465 Remote Similarity NPC477145
0.6465 Remote Similarity NPC473741
0.6442 Remote Similarity NPC477539
0.6415 Remote Similarity NPC155230
0.6415 Remote Similarity NPC322966
0.6415 Remote Similarity NPC275715
0.6403 Remote Similarity NPC471820
0.6403 Remote Similarity NPC471821
0.64 Remote Similarity NPC312315
0.6392 Remote Similarity NPC126186
0.6392 Remote Similarity NPC161774
0.6392 Remote Similarity NPC266888
0.6392 Remote Similarity NPC209156
0.6392 Remote Similarity NPC256312
0.6383 Remote Similarity NPC162104
0.6373 Remote Similarity NPC84128
0.6373 Remote Similarity NPC53858
0.6357 Remote Similarity NPC129666
0.6341 Remote Similarity NPC469899
0.6331 Remote Similarity NPC329761
0.6331 Remote Similarity NPC225648
0.6321 Remote Similarity NPC473495
0.6321 Remote Similarity NPC324506
0.629 Remote Similarity NPC470652
0.6277 Remote Similarity NPC139326
0.6263 Remote Similarity NPC470782
0.623 Remote Similarity NPC296043
0.6222 Remote Similarity NPC68865
0.6214 Remote Similarity NPC145113
0.6207 Remote Similarity NPC128303
0.62 Remote Similarity NPC59867
0.6183 Remote Similarity NPC120335
0.6179 Remote Similarity NPC329216
0.6164 Remote Similarity NPC297145
0.6164 Remote Similarity NPC197743
0.6162 Remote Similarity NPC327272
0.6161 Remote Similarity NPC134504
0.6161 Remote Similarity NPC47076
0.6154 Remote Similarity NPC241394
0.6143 Remote Similarity NPC262077
0.614 Remote Similarity NPC233932
0.6121 Remote Similarity NPC265094
0.6115 Remote Similarity NPC52748
0.6115 Remote Similarity NPC476978
0.6102 Remote Similarity NPC271562
0.6098 Remote Similarity NPC473819
0.6094 Remote Similarity NPC470653
0.6094 Remote Similarity NPC470654
0.6094 Remote Similarity NPC470650
0.6091 Remote Similarity NPC315237
0.6082 Remote Similarity NPC478256
0.6074 Remote Similarity NPC248283
0.6071 Remote Similarity NPC313867
0.6071 Remote Similarity NPC316008
0.605 Remote Similarity NPC15413
0.6043 Remote Similarity NPC161069
0.6034 Remote Similarity NPC474244
0.6028 Remote Similarity NPC314358
0.602 Remote Similarity NPC470781
0.6014 Remote Similarity NPC268841
0.6014 Remote Similarity NPC163392
0.6014 Remote Similarity NPC239762
0.6014 Remote Similarity NPC46098
0.6014 Remote Similarity NPC307357
0.6 Remote Similarity NPC474312
0.6 Remote Similarity NPC315283
0.6 Remote Similarity NPC128005
0.6 Remote Similarity NPC84182
0.6 Remote Similarity NPC314388
0.5985 Remote Similarity NPC127741
0.5984 Remote Similarity NPC477238
0.5984 Remote Similarity NPC160688
0.5979 Remote Similarity NPC474812
0.5969 Remote Similarity NPC36254
0.5969 Remote Similarity NPC252878
0.5957 Remote Similarity NPC315266
0.5954 Remote Similarity NPC470651
0.5954 Remote Similarity NPC470655
0.5944 Remote Similarity NPC105717
0.5932 Remote Similarity NPC64168
0.5923 Remote Similarity NPC6975
0.5923 Remote Similarity NPC46427
0.5917 Remote Similarity NPC474099
0.5903 Remote Similarity NPC2501
0.5897 Remote Similarity NPC471258
0.5891 Remote Similarity NPC202521
0.5891 Remote Similarity NPC50520
0.5888 Remote Similarity NPC475975
0.5882 Remote Similarity NPC287401
0.5882 Remote Similarity NPC475918
0.5874 Remote Similarity NPC138775
0.5862 Remote Similarity NPC475168
0.5862 Remote Similarity NPC7817
0.5859 Remote Similarity NPC245534
0.5857 Remote Similarity NPC469426
0.5857 Remote Similarity NPC168113
0.5857 Remote Similarity NPC469427
0.5849 Remote Similarity NPC235078
0.5847 Remote Similarity NPC173690
0.5847 Remote Similarity NPC279833
0.5847 Remote Similarity NPC6271
0.5847 Remote Similarity NPC471260
0.5847 Remote Similarity NPC80439
0.5827 Remote Similarity NPC315210
0.5827 Remote Similarity NPC315848
0.5827 Remote Similarity NPC477237
0.5816 Remote Similarity NPC197682
0.5816 Remote Similarity NPC322274
0.5816 Remote Similarity NPC176226
0.5814 Remote Similarity NPC200964
0.5814 Remote Similarity NPC476990
0.5809 Remote Similarity NPC246079
0.58 Remote Similarity NPC141325
0.5794 Remote Similarity NPC472351
0.5789 Remote Similarity NPC117829
0.5782 Remote Similarity NPC122590
0.5782 Remote Similarity NPC286551
0.5776 Remote Similarity NPC158394
0.5772 Remote Similarity NPC316984
0.5772 Remote Similarity NPC30911
0.5769 Remote Similarity NPC474833
0.5758 Remote Similarity NPC476285
0.5758 Remote Similarity NPC476291
0.575 Remote Similarity NPC471259
0.5743 Remote Similarity NPC470902
0.5743 Remote Similarity NPC138435
0.5743 Remote Similarity NPC43219
0.5735 Remote Similarity NPC130309

  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 NPC13175 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
0.6768 Remote Similarity NPD7763 Phase 2
0.6768 Remote Similarity NPD7762 Phase 2
0.6765 Remote Similarity NPD7760 Phase 2
0.6765 Remote Similarity NPD7759 Phase 2
0.6762 Remote Similarity NPD4261 Phase 1
0.6762 Remote Similarity NPD4780 Clinical (unspecified phase)
0.6549 Remote Similarity NPD6122 Discontinued
0.6545 Remote Similarity NPD8038 Phase 2
0.6522 Remote Similarity NPD2147 Approved
0.6489 Remote Similarity NPD7840 Approved
0.6476 Remote Similarity NPD3177 Phase 3
0.6442 Remote Similarity NPD3723 Clinical (unspecified phase)
0.6373 Remote Similarity NPD2683 Discontinued
0.6364 Remote Similarity NPD7841 Clinical (unspecified phase)
0.6214 Remote Similarity NPD1125 Discovery
0.6106 Remote Similarity NPD3714 Approved
0.6106 Remote Similarity NPD3713 Approved
0.6106 Remote Similarity NPD3715 Approved
0.6047 Remote Similarity NPD2584 Suspended
0.6036 Remote Similarity NPD5781 Clinical (unspecified phase)
0.6029 Remote Similarity NPD7113 Clinical (unspecified phase)
0.6 Remote Similarity NPD6120 Clinical (unspecified phase)
0.5985 Remote Similarity NPD8173 Phase 2
0.5985 Remote Similarity NPD8172 Phase 2
0.596 Remote Similarity NPD265 Phase 3
0.596 Remote Similarity NPD266 Phase 3
0.5882 Remote Similarity NPD1428 Phase 2
0.5882 Remote Similarity NPD1385 Discontinued
0.5856 Remote Similarity NPD6094 Approved
0.5856 Remote Similarity NPD6095 Approved
0.582 Remote Similarity NPD1805 Phase 2
0.582 Remote Similarity NPD1804 Phase 2
0.5794 Remote Similarity NPD9577 Approved
0.5794 Remote Similarity NPD3733 Clinical (unspecified phase)
0.5772 Remote Similarity NPD2204 Approved
0.5758 Remote Similarity NPD2220 Clinical (unspecified phase)
0.5748 Remote Similarity NPD2099 Approved
0.5688 Remote Similarity NPD5791 Phase 2
0.5688 Remote Similarity NPD9512 Approved
0.5672 Remote Similarity NPD2585 Clinical (unspecified phase)
0.5664 Remote Similarity NPD1686 Approved
0.5655 Remote Similarity NPD2055 Phase 3
0.5655 Remote Similarity NPD2054 Approved
0.5635 Remote Similarity NPD1000 Clinical (unspecified phase)
0.5635 Remote Similarity NPD2100 Approved
0.5625 Remote Similarity NPD1773 Discontinued
0.5619 Remote Similarity NPD4815 Discontinued
0.56 Remote Similarity NPD9649 Approved
0.56 Remote Similarity NPD2090 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