Structure

Physi-Chem Properties

Molecular Weight:  521.18
Volume:  470.717
LogP:  -0.364
LogD:  -0.125
LogS:  -1.256
# Rotatable Bonds:  6
TPSA:  211.33
# H-Bond Aceptor:  15
# H-Bond Donor:  5
# Rings:  5
# Heavy Atoms:  15

MedChem Properties

QED Drug-Likeness Score:  0.222
Synthetic Accessibility Score:  5.465
Fsp3:  0.591
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:  -6.282
MDCK Permeability:  5.815025724587031e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.99
Human Intestinal Absorption (HIA):  0.931
20% Bioavailability (F20%):  0.129
30% Bioavailability (F30%):  0.99

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.3
Plasma Protein Binding (PPB):  29.717796325683594%
Volume Distribution (VD):  1.165
Pgp-substrate:  62.79803466796875%

ADMET: Metabolism

CYP1A2-inhibitor:  0.027
CYP1A2-substrate:  0.808
CYP2C19-inhibitor:  0.153
CYP2C19-substrate:  0.063
CYP2C9-inhibitor:  0.01
CYP2C9-substrate:  0.019
CYP2D6-inhibitor:  0.02
CYP2D6-substrate:  0.05
CYP3A4-inhibitor:  0.076
CYP3A4-substrate:  0.114

ADMET: Excretion

Clearance (CL):  4.173
Half-life (T1/2):  0.856

ADMET: Toxicity

hERG Blockers:  0.096
Human Hepatotoxicity (H-HT):  0.985
Drug-inuced Liver Injury (DILI):  0.987
AMES Toxicity:  0.182
Rat Oral Acute Toxicity:  0.395
Maximum Recommended Daily Dose:  0.121
Skin Sensitization:  0.301
Carcinogencity:  0.024
Eye Corrosion:  0.003
Eye Irritation:  0.01
Respiratory Toxicity:  0.751

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

  Natural Product: NPC276373

Natural Product ID:  NPC276373
Common Name*:   LUHFPLRYWUPHKS-ORBSYVJISA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  LUHFPLRYWUPHKS-ORBSYVJISA-N
Standard InCHI:  InChI=1S/C22H27N5O10/c1-4-8(2)20(30)36-16-12(28)15(21(31)33-3)35-10-5-9-14(37-22(10,16)32)13(29)19(34-9)27-7-26-11-17(23)24-6-25-18(11)27/h4,6-7,9-10,12-16,19,28-29,32H,5H2,1-3H3,(H2,23,24,25)/b8-4+/t9-,10-,12-,13-,14+,15+,16+,19-,22-/m1/s1
SMILES:  C/C=C(C)/C(=O)O[C@H]1[C@@H]([C@@H](C(=O)OC)O[C@@H]2C[C@@H]3[C@@H]([C@H]([C@H](n4cnc5c(N)ncnc45)O3)O)O[C@@]12O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL3109445
PubChem CID:   76317500
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates
          • [CHEMONTID:0002105] Glycosyl compounds
            • [CHEMONTID:0002203] Glycosylamines

*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
NPO32887 Streptomyces sp. L-9-10 Species Streptomycetaceae Bacteria organic extract n.a. n.a. PMID[24533857]
NPO40215 Streptomyces sp. CB01388 Strain Streptomycetaceae Bacteria n.a. n.a. n.a. PMID[29469575]

☑ 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
NPT71 Cell Line HEK293 Homo sapiens IC50 = 2200.0 nM PMID[476526]
NPT180 Cell Line HCT-8 Homo sapiens EC50 > 25000.0 nM PMID[476527]
NPT2615 Cell Line HEK-293T Homo sapiens CC50 > 40000.0 nM PMID[476527]
NPT65 Cell Line HepG2 Homo sapiens CC50 > 40000.0 nM PMID[476527]
NPT2 Others Unspecified IC50 = 4900.0 nM PMID[476526]
NPT2 Others Unspecified Inhibition = 42.3 % PMID[476526]
NPT2 Others Unspecified Inhibition = 92.4 % PMID[476526]
NPT1022 Organism Cryptosporidium parvum Cryptosporidium parvum EC50 = 2700.0 nM PMID[476527]
NPT1022 Organism Cryptosporidium parvum Cryptosporidium parvum EC50 = 2800.0 nM PMID[476527]

☑ 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 NPC276373 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
0.9944 High Similarity NPC5802
0.9889 High Similarity NPC157821
0.9218 High Similarity NPC282458
0.9218 High Similarity NPC78941
0.905 High Similarity NPC24589
0.7742 Intermediate Similarity NPC290959
0.7541 Intermediate Similarity NPC239737
0.7333 Intermediate Similarity NPC219313
0.7278 Intermediate Similarity NPC189068
0.7238 Intermediate Similarity NPC309832
0.7222 Intermediate Similarity NPC107374
0.7222 Intermediate Similarity NPC21448
0.7222 Intermediate Similarity NPC156461
0.7191 Intermediate Similarity NPC317821
0.7182 Intermediate Similarity NPC164665
0.7173 Intermediate Similarity NPC325906
0.7143 Intermediate Similarity NPC269827
0.712 Intermediate Similarity NPC150853
0.712 Intermediate Similarity NPC324484
0.7114 Intermediate Similarity NPC313514
0.7111 Intermediate Similarity NPC229974
0.7097 Intermediate Similarity NPC212551
0.7097 Intermediate Similarity NPC302778
0.7068 Intermediate Similarity NPC323091
0.7059 Intermediate Similarity NPC174802
0.7041 Intermediate Similarity NPC313897
0.7021 Intermediate Similarity NPC224076
0.7005 Intermediate Similarity NPC130586
0.7005 Intermediate Similarity NPC164952
0.7 Intermediate Similarity NPC161659
0.7 Intermediate Similarity NPC209525
0.6989 Remote Similarity NPC185991
0.6989 Remote Similarity NPC211025
0.6989 Remote Similarity NPC85689
0.6984 Remote Similarity NPC226245
0.6952 Remote Similarity NPC321814
0.6952 Remote Similarity NPC472816
0.6944 Remote Similarity NPC129756
0.6923 Remote Similarity NPC314152
0.6898 Remote Similarity NPC161224
0.6895 Remote Similarity NPC316618
0.6882 Remote Similarity NPC136349
0.6862 Remote Similarity NPC207633
0.6828 Remote Similarity NPC121222
0.6784 Remote Similarity NPC326529
0.6772 Remote Similarity NPC328479
0.6771 Remote Similarity NPC195140
0.675 Remote Similarity NPC189261
0.675 Remote Similarity NPC319100
0.675 Remote Similarity NPC324198
0.6719 Remote Similarity NPC54320
0.6719 Remote Similarity NPC313754
0.6719 Remote Similarity NPC311197
0.6703 Remote Similarity NPC33996
0.6667 Remote Similarity NPC52238
0.6667 Remote Similarity NPC326082
0.6632 Remote Similarity NPC93365
0.6566 Remote Similarity NPC261595
0.6533 Remote Similarity NPC324033
0.6533 Remote Similarity NPC321458
0.6503 Remote Similarity NPC320818
0.6425 Remote Similarity NPC321052
0.6395 Remote Similarity NPC21461
0.6395 Remote Similarity NPC160666
0.6364 Remote Similarity NPC265111
0.6329 Remote Similarity NPC473585
0.6327 Remote Similarity NPC472833
0.6316 Remote Similarity NPC250178
0.6313 Remote Similarity NPC18308
0.6313 Remote Similarity NPC472832
0.6193 Remote Similarity NPC472834
0.616 Remote Similarity NPC150447
0.6154 Remote Similarity NPC326694
0.615 Remote Similarity NPC61198
0.6109 Remote Similarity NPC158055
0.6101 Remote Similarity NPC233431
0.6101 Remote Similarity NPC300139
0.6096 Remote Similarity NPC262926
0.6085 Remote Similarity NPC30326
0.6075 Remote Similarity NPC57279
0.6068 Remote Similarity NPC222174
0.6062 Remote Similarity NPC274384
0.6062 Remote Similarity NPC89147
0.6059 Remote Similarity NPC107160
0.6049 Remote Similarity NPC168702
0.6049 Remote Similarity NPC125659
0.6031 Remote Similarity NPC232408
0.6031 Remote Similarity NPC64705
0.6029 Remote Similarity NPC164845
0.601 Remote Similarity NPC251233
0.601 Remote Similarity NPC211820
0.6 Remote Similarity NPC33382
0.6 Remote Similarity NPC144474
0.6 Remote Similarity NPC133782
0.6 Remote Similarity NPC527
0.5979 Remote Similarity NPC317746
0.5979 Remote Similarity NPC177169
0.5957 Remote Similarity NPC319221
0.5931 Remote Similarity NPC14590
0.5928 Remote Similarity NPC318590
0.5911 Remote Similarity NPC103388
0.5907 Remote Similarity NPC186619
0.5904 Remote Similarity NPC324009
0.5876 Remote Similarity NPC74306
0.5876 Remote Similarity NPC315642
0.5863 Remote Similarity NPC324815
0.5833 Remote Similarity NPC101676
0.5805 Remote Similarity NPC321393
0.5798 Remote Similarity NPC246193
0.5737 Remote Similarity NPC315126
0.5737 Remote Similarity NPC314774
0.5722 Remote Similarity NPC296437
0.5714 Remote Similarity NPC476528
0.5714 Remote Similarity NPC476433
0.5692 Remote Similarity NPC470266
0.5685 Remote Similarity NPC476522
0.5685 Remote Similarity NPC476520
0.5685 Remote Similarity NPC474986
0.5685 Remote Similarity NPC476013
0.5683 Remote Similarity NPC54537
0.5678 Remote Similarity NPC476408
0.5657 Remote Similarity NPC476521

  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 NPC276373 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
0.7772 Intermediate Similarity NPD5684 Clinical (unspecified phase)
0.7772 Intermediate Similarity NPD5682 Phase 3
0.7772 Intermediate Similarity NPD5683 Clinical (unspecified phase)
0.7377 Intermediate Similarity NPD3107 Discontinued
0.7287 Intermediate Similarity NPD3083 Approved
0.7258 Intermediate Similarity NPD2646 Discontinued
0.7222 Intermediate Similarity NPD249 Approved
0.7222 Intermediate Similarity NPD250 Approved
0.7173 Intermediate Similarity NPD1776 Approved
0.7173 Intermediate Similarity NPD1777 Approved
0.7143 Intermediate Similarity NPD186 Discovery
0.7143 Intermediate Similarity NPD195 Approved
0.7128 Intermediate Similarity NPD5666 Phase 2
0.7114 Intermediate Similarity NPD7138 Phase 2
0.7083 Intermediate Similarity NPD7988 Suspended
0.7074 Intermediate Similarity NPD2624 Phase 2
0.7071 Intermediate Similarity NPD4716 Approved
0.7059 Intermediate Similarity NPD339 Approved
0.7047 Intermediate Similarity NPD2647 Phase 3
0.7035 Intermediate Similarity NPD4744 Clinical (unspecified phase)
0.7021 Intermediate Similarity NPD169 Phase 2
0.7005 Intermediate Similarity NPD1750 Clinical (unspecified phase)
0.7005 Intermediate Similarity NPD338 Approved
0.7005 Intermediate Similarity NPD1369 Phase 2
0.6989 Remote Similarity NPD283 Approved
0.6923 Remote Similarity NPD185 Approved
0.6915 Remote Similarity NPD242 Approved
0.6897 Remote Similarity NPD6417 Clinical (unspecified phase)
0.6895 Remote Similarity NPD1732 Phase 3
0.6882 Remote Similarity NPD548 Clinical (unspecified phase)
0.6875 Remote Similarity NPD516 Clinical (unspecified phase)
0.6848 Remote Similarity NPD166 Approved
0.6813 Remote Similarity NPD193 Suspended
0.6803 Remote Similarity NPD6023 Discontinued
0.6755 Remote Similarity NPD3708 Phase 2
0.675 Remote Similarity NPD4171 Clinical (unspecified phase)
0.6719 Remote Similarity NPD219 Phase 3
0.6719 Remote Similarity NPD218 Approved
0.6719 Remote Similarity NPD220 Clinical (unspecified phase)
0.6719 Remote Similarity NPD216 Approved
0.6719 Remote Similarity NPD217 Approved
0.6716 Remote Similarity NPD1692 Approved
0.6695 Remote Similarity NPD8375 Approved
0.6695 Remote Similarity NPD8291 Clinical (unspecified phase)
0.6639 Remote Similarity NPD8371 Clinical (unspecified phase)
0.6632 Remote Similarity NPD546 Clinical (unspecified phase)
0.662 Remote Similarity NPD2965 Clinical (unspecified phase)
0.6592 Remote Similarity NPD5080 Phase 2
0.6578 Remote Similarity NPD7158 Phase 1
0.6566 Remote Similarity NPD247 Clinical (unspecified phase)
0.6562 Remote Similarity NPD214 Approved
0.6562 Remote Similarity NPD213 Clinical (unspecified phase)
0.6552 Remote Similarity NPD1412 Clinical (unspecified phase)
0.6547 Remote Similarity NPD5079 Phase 2
0.6514 Remote Similarity NPD2877 Clinical (unspecified phase)
0.6514 Remote Similarity NPD2876 Phase 3
0.6486 Remote Similarity NPD2902 Phase 2
0.6486 Remote Similarity NPD2903 Clinical (unspecified phase)
0.6455 Remote Similarity NPD2824 Phase 2
0.6409 Remote Similarity NPD248 Discontinued
0.6398 Remote Similarity NPD4054 Clinical (unspecified phase)
0.6364 Remote Similarity NPD7323 Phase 2
0.6351 Remote Similarity NPD2630 Approved
0.6351 Remote Similarity NPD2631 Clinical (unspecified phase)
0.6351 Remote Similarity NPD2632 Approved
0.6349 Remote Similarity NPD4240 Approved
0.6329 Remote Similarity NPD8409 Suspended
0.6316 Remote Similarity NPD171 Discontinued
0.6313 Remote Similarity NPD5665 Clinical (unspecified phase)
0.6289 Remote Similarity NPD7842 Phase 2
0.6277 Remote Similarity NPD549 Approved
0.6277 Remote Similarity NPD3696 Approved
0.6277 Remote Similarity NPD3695 Approved
0.623 Remote Similarity NPD9632 Phase 3
0.615 Remote Similarity NPD252 Clinical (unspecified phase)
0.612 Remote Similarity NPD870 Clinical (unspecified phase)
0.6109 Remote Similarity NPD6840 Approved
0.6091 Remote Similarity NPD536 Clinical (unspecified phase)
0.608 Remote Similarity NPD8373 Clinical (unspecified phase)
0.6048 Remote Similarity NPD1046 Clinical (unspecified phase)
0.602 Remote Similarity NPD4074 Clinical (unspecified phase)
0.6 Remote Similarity NPD7531 Clinical (unspecified phase)
0.6 Remote Similarity NPD9633 Phase 3
0.5992 Remote Similarity NPD8250 Phase 2
0.599 Remote Similarity NPD1430 Approved
0.599 Remote Similarity NPD3085 Phase 1
0.599 Remote Similarity NPD1431 Approved
0.5966 Remote Similarity NPD4555 Clinical (unspecified phase)
0.5965 Remote Similarity NPD4495 Phase 1
0.596 Remote Similarity NPD3086 Phase 3
0.5944 Remote Similarity NPD7850 Discontinued
0.5944 Remote Similarity NPD7851 Phase 1
0.5939 Remote Similarity NPD6763 Discontinued
0.5938 Remote Similarity NPD5486 Discontinued
0.593 Remote Similarity NPD9605 Phase 3
0.5926 Remote Similarity NPD194 Clinical (unspecified phase)
0.5899 Remote Similarity NPD2152 Clinical (unspecified phase)
0.5893 Remote Similarity NPD4458 Phase 2
0.5893 Remote Similarity NPD4459 Clinical (unspecified phase)
0.588 Remote Similarity NPD1063 Phase 2
0.5876 Remote Similarity NPD582 Approved
0.5859 Remote Similarity NPD5458 Discontinued
0.584 Remote Similarity NPD4896 Clinical (unspecified phase)
0.5838 Remote Similarity NPD9408 Phase 3
0.5833 Remote Similarity NPD1808 Phase 1
0.5826 Remote Similarity NPD5072 Discontinued
0.5787 Remote Similarity NPD1730 Discontinued
0.5781 Remote Similarity NPD6381 Phase 2
0.5771 Remote Similarity NPD34 Approved
0.5771 Remote Similarity NPD4714 Approved
0.5771 Remote Similarity NPD231 Clinical (unspecified phase)
0.5771 Remote Similarity NPD4713 Clinical (unspecified phase)
0.5771 Remote Similarity NPD4715 Clinical (unspecified phase)
0.5768 Remote Similarity NPD1571 Phase 2
0.5756 Remote Similarity NPD6036 Suspended
0.5755 Remote Similarity NPD8421 Discontinued
0.5729 Remote Similarity NPD1121 Approved
0.5729 Remote Similarity NPD1120 Approved
0.5714 Remote Similarity NPD6351 Discovery
0.5714 Remote Similarity NPD7502 Clinical (unspecified phase)
0.57 Remote Similarity NPD2593 Clinical (unspecified phase)
0.5697 Remote Similarity NPD1572 Phase 2
0.5697 Remote Similarity NPD7486 Phase 1
0.5696 Remote Similarity NPD2453 Phase 2
0.5696 Remote Similarity NPD2451 Phase 2
0.5696 Remote Similarity NPD2452 Phase 2
0.5696 Remote Similarity NPD2450 Phase 2
0.5685 Remote Similarity NPD5887 Clinical (unspecified phase)
0.568 Remote Similarity NPD5321 Phase 3
0.5678 Remote Similarity NPD8271 Discontinued
0.5676 Remote Similarity NPD4950 Approved
0.5663 Remote Similarity NPD2253 Discontinued
0.5657 Remote Similarity NPD7197 Approved
0.565 Remote Similarity NPD8329 Phase 3
0.5644 Remote Similarity NPD353 Discontinued
0.5633 Remote Similarity NPD8119 Discontinued
0.5625 Remote Similarity NPD8370 Discontinued
0.5612 Remote Similarity NPD8327 Clinical (unspecified phase)
0.5612 Remote Similarity NPD8326 Phase 3
0.5612 Remote Similarity NPD8325 Phase 3
0.5609 Remote Similarity NPD7103 Approved
0.5607 Remote Similarity NPD3590 Clinical (unspecified phase)
0.5607 Remote Similarity NPD5827 Discontinued
0.5602 Remote Similarity NPD282 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