Structure

Physi-Chem Properties

Molecular Weight:  593.38
Volume:  611.02
LogP:  2.399
LogD:  2.251
LogS:  -3.517
# Rotatable Bonds:  5
TPSA:  145.43
# H-Bond Aceptor:  12
# H-Bond Donor:  2
# Rings:  2
# Heavy Atoms:  12

MedChem Properties

QED Drug-Likeness Score:  0.457
Synthetic Accessibility Score:  5.065
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:  -5.239
MDCK Permeability:  1.1288981113466434e-05
Pgp-inhibitor:  0.994
Pgp-substrate:  0.951
Human Intestinal Absorption (HIA):  0.145
20% Bioavailability (F20%):  0.013
30% Bioavailability (F30%):  0.661

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.177
Plasma Protein Binding (PPB):  78.16702270507812%
Volume Distribution (VD):  0.529
Pgp-substrate:  23.840496063232422%

ADMET: Metabolism

CYP1A2-inhibitor:  0.002
CYP1A2-substrate:  0.046
CYP2C19-inhibitor:  0.075
CYP2C19-substrate:  0.651
CYP2C9-inhibitor:  0.064
CYP2C9-substrate:  0.076
CYP2D6-inhibitor:  0.014
CYP2D6-substrate:  0.087
CYP3A4-inhibitor:  0.804
CYP3A4-substrate:  0.619

ADMET: Excretion

Clearance (CL):  6.814
Half-life (T1/2):  0.743

ADMET: Toxicity

hERG Blockers:  0.002
Human Hepatotoxicity (H-HT):  0.923
Drug-inuced Liver Injury (DILI):  0.924
AMES Toxicity:  0.008
Rat Oral Acute Toxicity:  0.507
Maximum Recommended Daily Dose:  0.321
Skin Sensitization:  0.063
Carcinogencity:  0.012
Eye Corrosion:  0.003
Eye Irritation:  0.005
Respiratory Toxicity:  0.014

Download Data

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

  Natural Product: NPC173763

Natural Product ID:  NPC173763
Common Name*:   Destruxin B
IUPAC Name:   (3S,10S,13S,16S,19S)-16-[(2S)-butan-2-yl]-10,11,14-trimethyl-3-(2-methylpropyl)-13-propan-2-yl-4-oxa-1,8,11,14,17-pentazabicyclo[17.3.0]docosane-2,5,9,12,15,18-hexone
Synonyms:   destruxin B
Standard InCHIKey:  GNBHVMBELHWUIF-BKWLFHPQSA-N
Standard InCHI:  InChI=1S/C30H51N5O7/c1-10-19(6)24-29(40)34(9)25(18(4)5)30(41)33(8)20(7)26(37)31-14-13-23(36)42-22(16-17(2)3)28(39)35-15-11-12-21(35)27(38)32-24/h17-22,24-25H,10-16H2,1-9H3,(H,31,37)(H,32,38)/t19-,20-,21-,22-,24-,25-/m0/s1
SMILES:  CC[C@@H]([C@@H]1N=C(O)[C@@H]2CCCN2C(=O)[C@H](CC(C)C)OC(=O)CCN=C([C@@H](N(C(=O)[C@@H](N(C1=O)C)C(C)C)C)C)O)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2372205
PubChem CID:   23306078
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]
NPO9967 Metarhizium anisopliae Species Clavicipitaceae Eukaryota n.a. n.a. n.a. PMID[7623030]
NPO33484 os-f68576 n.a. n.a. n.a. n.a. n.a. n.a. PMID[9514014]
NPO9967 Metarhizium anisopliae Species Clavicipitaceae 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
NPT2 Others Unspecified Activity = 2 nM PMID[20719504]
NPT2 Others Unspecified Ratio = 19 n.a. PMID[25136754]
NPT2 Others Unspecified Activity = 35 mU/ml PMID[25136754]
NPT963 Organism Hepatitis B virus Hepatitis B virus IC50 = 0.2 ug/ml PMID[26860736]
NPT419 Organism Oryctolagus cuniculus Oryctolagus cuniculus IC50 > 1000000 nM PubChem BioAssay data set

☑ 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 NPC173763 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 NPC471098
1.0 High Similarity NPC62263
0.9882 High Similarity NPC474576
0.9765 High Similarity NPC474593
0.9765 High Similarity NPC475801
0.8925 High Similarity NPC475440
0.8842 High Similarity NPC475149
0.8842 High Similarity NPC471097
0.8632 High Similarity NPC475791
0.8632 High Similarity NPC13175
0.8571 High Similarity NPC475637
0.8526 High Similarity NPC475758
0.8526 High Similarity NPC220234
0.8283 Intermediate Similarity NPC323720
0.8265 Intermediate Similarity NPC5864
0.8265 Intermediate Similarity NPC301148
0.8265 Intermediate Similarity NPC124554
0.8125 Intermediate Similarity NPC473597
0.81 Intermediate Similarity NPC124549
0.8 Intermediate Similarity NPC198344
0.7864 Intermediate Similarity NPC67009
0.7864 Intermediate Similarity NPC171734
0.7789 Intermediate Similarity NPC477538
0.7789 Intermediate Similarity NPC476019
0.7667 Intermediate Similarity NPC470783
0.7582 Intermediate Similarity NPC246005
0.7556 Intermediate Similarity NPC476156
0.7556 Intermediate Similarity NPC476137
0.7556 Intermediate Similarity NPC476117
0.7556 Intermediate Similarity NPC476243
0.7473 Intermediate Similarity NPC476302
0.7471 Intermediate Similarity NPC178919
0.7471 Intermediate Similarity NPC263281
0.7444 Intermediate Similarity NPC31756
0.7396 Intermediate Similarity NPC322966
0.7391 Intermediate Similarity NPC84128
0.7391 Intermediate Similarity NPC53858
0.7339 Intermediate Similarity NPC471202
0.7339 Intermediate Similarity NPC63191
0.7333 Intermediate Similarity NPC477145
0.7333 Intermediate Similarity NPC473741
0.7283 Intermediate Similarity NPC475542
0.7273 Intermediate Similarity NPC209156
0.7273 Intermediate Similarity NPC256312
0.7273 Intermediate Similarity NPC161774
0.7273 Intermediate Similarity NPC266888
0.7253 Intermediate Similarity NPC312315
0.7093 Intermediate Similarity NPC10716
0.7083 Intermediate Similarity NPC477539
0.7059 Intermediate Similarity NPC134504
0.7059 Intermediate Similarity NPC47076
0.7045 Intermediate Similarity NPC76297
0.7045 Intermediate Similarity NPC214532
0.7045 Intermediate Similarity NPC196007
0.7011 Intermediate Similarity NPC29598
0.7011 Intermediate Similarity NPC212866
0.7009 Intermediate Similarity NPC241394
0.7 Intermediate Similarity NPC315237
0.7 Intermediate Similarity NPC476875
0.7 Intermediate Similarity NPC327272
0.6932 Remote Similarity NPC478256
0.6916 Remote Similarity NPC128303
0.6889 Remote Similarity NPC126186
0.6869 Remote Similarity NPC275715
0.6848 Remote Similarity NPC59867
0.6752 Remote Similarity NPC477238
0.6739 Remote Similarity NPC470782
0.6724 Remote Similarity NPC469899
0.6701 Remote Similarity NPC472351
0.6667 Remote Similarity NPC476877
0.6641 Remote Similarity NPC98424
0.6641 Remote Similarity NPC470884
0.6641 Remote Similarity NPC178662
0.6641 Remote Similarity NPC92784
0.6641 Remote Similarity NPC476133
0.6636 Remote Similarity NPC188785
0.661 Remote Similarity NPC315188
0.6581 Remote Similarity NPC477237
0.6562 Remote Similarity NPC471265
0.6562 Remote Similarity NPC471264
0.6545 Remote Similarity NPC476876
0.6522 Remote Similarity NPC43219
0.6522 Remote Similarity NPC138435
0.6522 Remote Similarity NPC103391
0.6522 Remote Similarity NPC472536
0.6484 Remote Similarity NPC470781
0.6477 Remote Similarity NPC84182
0.6477 Remote Similarity NPC128005
0.6452 Remote Similarity NPC86064
0.6444 Remote Similarity NPC322274
0.6429 Remote Similarity NPC235078
0.6413 Remote Similarity NPC141325
0.6392 Remote Similarity NPC23984
0.6391 Remote Similarity NPC209509
0.6387 Remote Similarity NPC470652
0.6383 Remote Similarity NPC476324
0.6383 Remote Similarity NPC476130
0.6374 Remote Similarity NPC476285
0.6374 Remote Similarity NPC476291
0.6364 Remote Similarity NPC145748
0.6364 Remote Similarity NPC95478
0.6364 Remote Similarity NPC155670
0.6327 Remote Similarity NPC184473
0.6325 Remote Similarity NPC296043
0.6321 Remote Similarity NPC117829
0.6311 Remote Similarity NPC470653
0.6311 Remote Similarity NPC470654
0.6311 Remote Similarity NPC470650
0.63 Remote Similarity NPC227051
0.6292 Remote Similarity NPC287693
0.6288 Remote Similarity NPC263493
0.6288 Remote Similarity NPC269398
0.6283 Remote Similarity NPC207820
0.6275 Remote Similarity NPC473495
0.6275 Remote Similarity NPC52533
0.6271 Remote Similarity NPC329216
0.626 Remote Similarity NPC309525
0.625 Remote Similarity NPC233108
0.625 Remote Similarity NPC240848
0.6226 Remote Similarity NPC280066
0.6198 Remote Similarity NPC160688
0.618 Remote Similarity NPC160661
0.617 Remote Similarity NPC476248
0.617 Remote Similarity NPC320221
0.6162 Remote Similarity NPC6902
0.6162 Remote Similarity NPC284456
0.6161 Remote Similarity NPC205176
0.6148 Remote Similarity NPC5620
0.6146 Remote Similarity NPC472594
0.6136 Remote Similarity NPC243964
0.6132 Remote Similarity NPC301010
0.6087 Remote Similarity NPC314273
0.6087 Remote Similarity NPC193280
0.6067 Remote Similarity NPC57420
0.6058 Remote Similarity NPC155230
0.6032 Remote Similarity NPC470655
0.6032 Remote Similarity NPC470651
0.6019 Remote Similarity NPC469739
0.6014 Remote Similarity NPC471820
0.6014 Remote Similarity NPC471821
0.6 Remote Similarity NPC477729
0.6 Remote Similarity NPC296143
0.6 Remote Similarity NPC128559
0.5978 Remote Similarity NPC306696
0.5971 Remote Similarity NPC129666
0.5968 Remote Similarity NPC50520
0.5938 Remote Similarity NPC472595
0.592 Remote Similarity NPC477518
0.5918 Remote Similarity NPC37681
0.5917 Remote Similarity NPC473819
0.59 Remote Similarity NPC314466
0.5895 Remote Similarity NPC29326
0.5891 Remote Similarity NPC120335
0.5887 Remote Similarity NPC162104
0.5882 Remote Similarity NPC139326
0.5865 Remote Similarity NPC477728
0.5833 Remote Similarity NPC38172
0.5827 Remote Similarity NPC225648
0.5827 Remote Similarity NPC329761
0.5825 Remote Similarity NPC277918
0.5821 Remote Similarity NPC68865
0.5818 Remote Similarity NPC313821
0.5814 Remote Similarity NPC313657
0.5795 Remote Similarity NPC473599
0.5793 Remote Similarity NPC297145
0.5793 Remote Similarity NPC197743
0.5789 Remote Similarity NPC265094
0.5778 Remote Similarity NPC105297
0.5776 Remote Similarity NPC271562
0.576 Remote Similarity NPC273185
0.5758 Remote Similarity NPC325902
0.5758 Remote Similarity NPC316242
0.5755 Remote Similarity NPC262077
0.5745 Remote Similarity NPC472579
0.573 Remote Similarity NPC327170
0.573 Remote Similarity NPC329564
0.5729 Remote Similarity NPC320865
0.5729 Remote Similarity NPC477641
0.5729 Remote Similarity NPC477643
0.5726 Remote Similarity NPC15413
0.5725 Remote Similarity NPC52748
0.5725 Remote Similarity NPC476978
0.5714 Remote Similarity NPC145658
0.5714 Remote Similarity NPC145113
0.5702 Remote Similarity NPC259586
0.57 Remote Similarity NPC315535
0.57 Remote Similarity NPC478017
0.57 Remote Similarity NPC315131
0.5684 Remote Similarity NPC477642
0.5683 Remote Similarity NPC316008
0.5683 Remote Similarity NPC313867
0.5672 Remote Similarity NPC248283
0.5667 Remote Similarity NPC314510
0.5667 Remote Similarity NPC477644
0.566 Remote Similarity NPC324506
0.5656 Remote Similarity NPC222481
0.5656 Remote Similarity NPC470621
0.5652 Remote Similarity NPC161069
0.5644 Remote Similarity NPC216090
0.5643 Remote Similarity NPC314358

  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 NPC173763 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
0.7634 Intermediate Similarity NPD7759 Phase 2
0.7634 Intermediate Similarity NPD7760 Phase 2
0.7473 Intermediate Similarity NPD7763 Phase 2
0.7473 Intermediate Similarity NPD7762 Phase 2
0.7423 Intermediate Similarity NPD4780 Clinical (unspecified phase)
0.7423 Intermediate Similarity NPD4261 Phase 1
0.7327 Intermediate Similarity NPD8038 Phase 2
0.7308 Intermediate Similarity NPD6122 Discontinued
0.7263 Intermediate Similarity NPD3723 Clinical (unspecified phase)
0.7204 Intermediate Similarity NPD2683 Discontinued
0.7113 Intermediate Similarity NPD3177 Phase 3
0.7021 Intermediate Similarity NPD1125 Discovery
0.7011 Intermediate Similarity NPD7840 Approved
0.699 Remote Similarity NPD3715 Approved
0.699 Remote Similarity NPD3714 Approved
0.699 Remote Similarity NPD3713 Approved
0.6961 Remote Similarity NPD7841 Clinical (unspecified phase)
0.6444 Remote Similarity NPD620 Approved
0.6408 Remote Similarity NPD2682 Approved
0.6389 Remote Similarity NPD6120 Clinical (unspecified phase)
0.6374 Remote Similarity NPD2220 Clinical (unspecified phase)
0.6364 Remote Similarity NPD3733 Clinical (unspecified phase)
0.6364 Remote Similarity NPD9577 Approved
0.6346 Remote Similarity NPD6699 Clinical (unspecified phase)
0.6339 Remote Similarity NPD6937 Approved
0.6264 Remote Similarity NPD3724 Clinical (unspecified phase)
0.6238 Remote Similarity NPD5791 Phase 2
0.6196 Remote Similarity NPD2697 Approved
0.6196 Remote Similarity NPD9649 Approved
0.6196 Remote Similarity NPD2695 Approved
0.6196 Remote Similarity NPD2696 Approved
0.6196 Remote Similarity NPD2694 Approved
0.6186 Remote Similarity NPD4815 Discontinued
0.6147 Remote Similarity NPD4825 Clinical (unspecified phase)
0.6146 Remote Similarity NPD2689 Clinical (unspecified phase)
0.6111 Remote Similarity NPD1784 Approved
0.6102 Remote Similarity NPD7916 Approved
0.6102 Remote Similarity NPD7915 Approved
0.6095 Remote Similarity NPD5792 Clinical (unspecified phase)
0.6042 Remote Similarity NPD1453 Phase 1
0.6019 Remote Similarity NPD3176 Clinical (unspecified phase)
0.5978 Remote Similarity NPD322 Phase 1
0.5887 Remote Similarity NPD7652 Discontinued
0.5826 Remote Similarity NPD1385 Discontinued
0.5818 Remote Similarity NPD3190 Approved
0.5818 Remote Similarity NPD3189 Approved
0.5818 Remote Similarity NPD3191 Approved
0.5814 Remote Similarity NPD1456 Approved
0.5804 Remote Similarity NPD5359 Clinical (unspecified phase)
0.58 Remote Similarity NPD9578 Clinical (unspecified phase)
0.5784 Remote Similarity NPD4829 Discontinued
0.575 Remote Similarity NPD8298 Phase 2
0.5729 Remote Similarity NPD2256 Clinical (unspecified phase)
0.57 Remote Similarity NPD7917 Clinical (unspecified phase)
0.57 Remote Similarity NPD7918 Clinical (unspecified phase)
0.5699 Remote Similarity NPD2263 Discontinued
0.5698 Remote Similarity NPD4276 Approved
0.5698 Remote Similarity NPD4277 Approved
0.5691 Remote Similarity NPD1773 Discontinued
0.5686 Remote Similarity NPD1448 Clinical (unspecified phase)
0.5684 Remote Similarity NPD1439 Clinical (unspecified phase)
0.5631 Remote Similarity NPD882 Phase 2
0.5631 Remote Similarity NPD883 Phase 2
0.563 Remote Similarity NPD7113 Clinical (unspecified phase)
0.563 Remote Similarity NPD1804 Phase 2
0.563 Remote Similarity NPD5767 Discontinued
0.563 Remote Similarity NPD4260 Discontinued
0.563 Remote Similarity NPD1805 Phase 2
0.5625 Remote Similarity NPD8041 Phase 2
0.5625 Remote Similarity NPD2584 Suspended
0.56 Remote Similarity NPD3160 Suspended
0.56 Remote Similarity NPD2645 Approved
0.56 Remote Similarity NPD4278 Clinical (unspecified phase)

  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