Structure

Physi-Chem Properties

Molecular Weight:  535.19
Volume:  488.013
LogP:  -0.02
LogD:  0.359
LogS:  -1.763
# Rotatable Bonds:  7
TPSA:  200.33
# H-Bond Aceptor:  15
# H-Bond Donor:  4
# Rings:  5
# Heavy Atoms:  15

MedChem Properties

QED Drug-Likeness Score:  0.264
Synthetic Accessibility Score:  5.49
Fsp3:  0.609
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:  -6.168
MDCK Permeability:  5.7268774980911985e-05
Pgp-inhibitor:  0.008
Pgp-substrate:  0.983
Human Intestinal Absorption (HIA):  0.947
20% Bioavailability (F20%):  0.033
30% Bioavailability (F30%):  0.982

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.311
Plasma Protein Binding (PPB):  28.10643768310547%
Volume Distribution (VD):  1.484
Pgp-substrate:  64.11998748779297%

ADMET: Metabolism

CYP1A2-inhibitor:  0.021
CYP1A2-substrate:  0.906
CYP2C19-inhibitor:  0.129
CYP2C19-substrate:  0.064
CYP2C9-inhibitor:  0.011
CYP2C9-substrate:  0.011
CYP2D6-inhibitor:  0.026
CYP2D6-substrate:  0.052
CYP3A4-inhibitor:  0.085
CYP3A4-substrate:  0.216

ADMET: Excretion

Clearance (CL):  6.649
Half-life (T1/2):  0.848

ADMET: Toxicity

hERG Blockers:  0.087
Human Hepatotoxicity (H-HT):  0.974
Drug-inuced Liver Injury (DILI):  0.987
AMES Toxicity:  0.106
Rat Oral Acute Toxicity:  0.394
Maximum Recommended Daily Dose:  0.071
Skin Sensitization:  0.211
Carcinogencity:  0.024
Eye Corrosion:  0.003
Eye Irritation:  0.01
Respiratory Toxicity:  0.633

Download Data

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

  Natural Product: NPC5802

Natural Product ID:  NPC5802
Common Name*:   PXURTMJWRXVZEJ-SYDSVXEMSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  PXURTMJWRXVZEJ-SYDSVXEMSA-N
Standard InCHI:  InChI=1S/C23H29N5O10/c1-5-9(2)21(30)37-17-13(29)15(22(31)34-4)36-11-6-10-14(38-23(11,17)32)16(33-3)20(35-10)28-8-27-12-18(24)25-7-26-19(12)28/h5,7-8,10-11,13-17,20,29,32H,6H2,1-4H3,(H2,24,25,26)/b9-5+/t10-,11-,13-,14+,15+,16-,17+,20-,23-/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)OC)O[C@@]12O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL3109450
PubChem CID:   6440493
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]

☑ 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 = 2300.0 nM PMID[448927]
NPT2 Others Unspecified IC50 = 500.0 nM PMID[448927]
NPT2 Others Unspecified Inhibition = 59.8 % PMID[448927]
NPT2 Others Unspecified Inhibition = 83.4 % PMID[448927]

☑ 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 NPC5802 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 NPC157821
0.9944 High Similarity NPC276373
0.9274 High Similarity NPC78941
0.9274 High Similarity NPC282458
0.9106 High Similarity NPC24589
0.7701 Intermediate Similarity NPC290959
0.75 Intermediate Similarity NPC239737
0.7293 Intermediate Similarity NPC309832
0.7293 Intermediate Similarity NPC219313
0.7238 Intermediate Similarity NPC189068
0.7182 Intermediate Similarity NPC156461
0.7182 Intermediate Similarity NPC21448
0.7182 Intermediate Similarity NPC107374
0.7164 Intermediate Similarity NPC313514
0.7151 Intermediate Similarity NPC317821
0.7143 Intermediate Similarity NPC164665
0.7135 Intermediate Similarity NPC325906
0.7104 Intermediate Similarity NPC269827
0.7092 Intermediate Similarity NPC313897
0.7083 Intermediate Similarity NPC324484
0.7081 Intermediate Similarity NPC150853
0.7072 Intermediate Similarity NPC229974
0.7059 Intermediate Similarity NPC302778
0.7059 Intermediate Similarity NPC212551
0.7031 Intermediate Similarity NPC323091
0.7021 Intermediate Similarity NPC174802
0.6984 Remote Similarity NPC224076
0.6968 Remote Similarity NPC130586
0.6968 Remote Similarity NPC164952
0.6961 Remote Similarity NPC209525
0.6961 Remote Similarity NPC161659
0.6952 Remote Similarity NPC185991
0.6952 Remote Similarity NPC85689
0.6952 Remote Similarity NPC211025
0.6947 Remote Similarity NPC226245
0.6915 Remote Similarity NPC472816
0.6915 Remote Similarity NPC321814
0.6906 Remote Similarity NPC129756
0.6885 Remote Similarity NPC314152
0.6862 Remote Similarity NPC161224
0.6859 Remote Similarity NPC316618
0.6845 Remote Similarity NPC136349
0.6825 Remote Similarity NPC207633
0.6791 Remote Similarity NPC121222
0.675 Remote Similarity NPC326529
0.6737 Remote Similarity NPC328479
0.6736 Remote Similarity NPC195140
0.6716 Remote Similarity NPC189261
0.6716 Remote Similarity NPC319100
0.6716 Remote Similarity NPC324198
0.6684 Remote Similarity NPC311197
0.6684 Remote Similarity NPC313754
0.6684 Remote Similarity NPC54320
0.6667 Remote Similarity NPC33996
0.6633 Remote Similarity NPC326082
0.6632 Remote Similarity NPC52238
0.6598 Remote Similarity NPC93365
0.6533 Remote Similarity NPC261595
0.65 Remote Similarity NPC324033
0.65 Remote Similarity NPC321458
0.6467 Remote Similarity NPC320818
0.6438 Remote Similarity NPC160666
0.6438 Remote Similarity NPC21461
0.6392 Remote Similarity NPC321052
0.6333 Remote Similarity NPC265111
0.6298 Remote Similarity NPC473585
0.6294 Remote Similarity NPC472833
0.6288 Remote Similarity NPC250178
0.6281 Remote Similarity NPC472832
0.6281 Remote Similarity NPC18308
0.62 Remote Similarity NPC150447
0.6162 Remote Similarity NPC472834
0.6122 Remote Similarity NPC326694
0.6117 Remote Similarity NPC61198
0.6083 Remote Similarity NPC158055
0.6073 Remote Similarity NPC233431
0.6073 Remote Similarity NPC300139
0.6064 Remote Similarity NPC262926
0.6053 Remote Similarity NPC30326
0.6043 Remote Similarity NPC57279
0.6039 Remote Similarity NPC222174
0.6034 Remote Similarity NPC107160
0.6031 Remote Similarity NPC89147
0.6031 Remote Similarity NPC274384
0.6019 Remote Similarity NPC125659
0.6019 Remote Similarity NPC168702
0.6 Remote Similarity NPC164845
0.6 Remote Similarity NPC232408
0.6 Remote Similarity NPC64705
0.5979 Remote Similarity NPC211820
0.5979 Remote Similarity NPC251233
0.5972 Remote Similarity NPC133782
0.5972 Remote Similarity NPC527
0.5972 Remote Similarity NPC144474
0.5971 Remote Similarity NPC33382
0.5956 Remote Similarity NPC103388
0.5949 Remote Similarity NPC177169
0.5949 Remote Similarity NPC317746
0.5926 Remote Similarity NPC319221
0.5904 Remote Similarity NPC324815
0.5902 Remote Similarity NPC14590
0.5897 Remote Similarity NPC318590
0.5876 Remote Similarity NPC186619
0.5873 Remote Similarity NPC324009
0.5846 Remote Similarity NPC315642
0.5846 Remote Similarity NPC74306
0.5806 Remote Similarity NPC101676
0.5777 Remote Similarity NPC321393
0.5777 Remote Similarity NPC314774
0.5777 Remote Similarity NPC315126
0.5767 Remote Similarity NPC246193
0.5692 Remote Similarity NPC296437
0.5685 Remote Similarity NPC476433
0.5685 Remote Similarity NPC476528
0.5663 Remote Similarity NPC470266
0.5658 Remote Similarity NPC54537
0.5657 Remote Similarity NPC476013
0.5657 Remote Similarity NPC476522
0.5657 Remote Similarity NPC476520
0.5657 Remote Similarity NPC474986
0.565 Remote Similarity NPC476408
0.5637 Remote Similarity NPC472436
0.5628 Remote Similarity NPC476521
0.561 Remote Similarity NPC168135
0.561 Remote Similarity NPC322800

  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 NPC5802 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
0.7732 Intermediate Similarity NPD5682 Phase 3
0.7732 Intermediate Similarity NPD5684 Clinical (unspecified phase)
0.7732 Intermediate Similarity NPD5683 Clinical (unspecified phase)
0.734 Intermediate Similarity NPD3083 Approved
0.7337 Intermediate Similarity NPD3107 Discontinued
0.7312 Intermediate Similarity NPD2646 Discontinued
0.7182 Intermediate Similarity NPD250 Approved
0.7182 Intermediate Similarity NPD249 Approved
0.7164 Intermediate Similarity NPD7138 Phase 2
0.7135 Intermediate Similarity NPD1777 Approved
0.7135 Intermediate Similarity NPD1776 Approved
0.7104 Intermediate Similarity NPD195 Approved
0.7104 Intermediate Similarity NPD186 Discovery
0.7092 Intermediate Similarity NPD5666 Phase 2
0.7059 Intermediate Similarity NPD1369 Phase 2
0.7047 Intermediate Similarity NPD7988 Suspended
0.7037 Intermediate Similarity NPD2624 Phase 2
0.7035 Intermediate Similarity NPD4716 Approved
0.7021 Intermediate Similarity NPD339 Approved
0.701 Intermediate Similarity NPD2647 Phase 3
0.7 Intermediate Similarity NPD4744 Clinical (unspecified phase)
0.6984 Remote Similarity NPD169 Phase 2
0.6968 Remote Similarity NPD338 Approved
0.6968 Remote Similarity NPD1750 Clinical (unspecified phase)
0.6952 Remote Similarity NPD283 Approved
0.6885 Remote Similarity NPD185 Approved
0.6878 Remote Similarity NPD242 Approved
0.6863 Remote Similarity NPD6417 Clinical (unspecified phase)
0.6859 Remote Similarity NPD1732 Phase 3
0.6845 Remote Similarity NPD548 Clinical (unspecified phase)
0.6839 Remote Similarity NPD516 Clinical (unspecified phase)
0.6811 Remote Similarity NPD166 Approved
0.6776 Remote Similarity NPD6023 Discontinued
0.6776 Remote Similarity NPD193 Suspended
0.6737 Remote Similarity NPD8375 Approved
0.6737 Remote Similarity NPD8291 Clinical (unspecified phase)
0.672 Remote Similarity NPD3708 Phase 2
0.6716 Remote Similarity NPD4171 Clinical (unspecified phase)
0.6684 Remote Similarity NPD216 Approved
0.6684 Remote Similarity NPD220 Clinical (unspecified phase)
0.6684 Remote Similarity NPD217 Approved
0.6684 Remote Similarity NPD219 Phase 3
0.6684 Remote Similarity NPD218 Approved
0.6683 Remote Similarity NPD1692 Approved
0.6681 Remote Similarity NPD8371 Clinical (unspecified phase)
0.6637 Remote Similarity NPD5080 Phase 2
0.6631 Remote Similarity NPD7158 Phase 1
0.6598 Remote Similarity NPD546 Clinical (unspecified phase)
0.6592 Remote Similarity NPD5079 Phase 2
0.659 Remote Similarity NPD2965 Clinical (unspecified phase)
0.6533 Remote Similarity NPD247 Clinical (unspecified phase)
0.6528 Remote Similarity NPD214 Approved
0.6528 Remote Similarity NPD213 Clinical (unspecified phase)
0.652 Remote Similarity NPD1412 Clinical (unspecified phase)
0.6484 Remote Similarity NPD2877 Clinical (unspecified phase)
0.6484 Remote Similarity NPD2876 Phase 3
0.6457 Remote Similarity NPD2903 Clinical (unspecified phase)
0.6457 Remote Similarity NPD2902 Phase 2
0.6445 Remote Similarity NPD4054 Clinical (unspecified phase)
0.6425 Remote Similarity NPD2824 Phase 2
0.6409 Remote Similarity NPD7323 Phase 2
0.6402 Remote Similarity NPD4240 Approved
0.6374 Remote Similarity NPD248 Discontinued
0.6371 Remote Similarity NPD8409 Suspended
0.634 Remote Similarity NPD7842 Phase 2
0.633 Remote Similarity NPD3695 Approved
0.633 Remote Similarity NPD3696 Approved
0.633 Remote Similarity NPD549 Approved
0.6321 Remote Similarity NPD2632 Approved
0.6321 Remote Similarity NPD2631 Clinical (unspecified phase)
0.6321 Remote Similarity NPD2630 Approved
0.6284 Remote Similarity NPD5665 Clinical (unspecified phase)
0.6283 Remote Similarity NPD171 Discontinued
0.6196 Remote Similarity NPD9632 Phase 3
0.6117 Remote Similarity NPD252 Clinical (unspecified phase)
0.6087 Remote Similarity NPD870 Clinical (unspecified phase)
0.6083 Remote Similarity NPD6840 Approved
0.6061 Remote Similarity NPD536 Clinical (unspecified phase)
0.6056 Remote Similarity NPD8373 Clinical (unspecified phase)
0.6054 Remote Similarity NPD9633 Phase 3
0.6042 Remote Similarity NPD1431 Approved
0.6042 Remote Similarity NPD1430 Approved
0.6019 Remote Similarity NPD1046 Clinical (unspecified phase)
0.599 Remote Similarity NPD4074 Clinical (unspecified phase)
0.5969 Remote Similarity NPD7531 Clinical (unspecified phase)
0.5968 Remote Similarity NPD8250 Phase 2
0.596 Remote Similarity NPD3085 Phase 1
0.5945 Remote Similarity NPD2152 Clinical (unspecified phase)
0.594 Remote Similarity NPD4555 Clinical (unspecified phase)
0.5939 Remote Similarity NPD4495 Phase 1
0.5938 Remote Similarity NPD4458 Phase 2
0.5938 Remote Similarity NPD4459 Clinical (unspecified phase)
0.593 Remote Similarity NPD3086 Phase 3
0.592 Remote Similarity NPD7850 Discontinued
0.592 Remote Similarity NPD7851 Phase 1
0.5913 Remote Similarity NPD6763 Discontinued
0.5911 Remote Similarity NPD5486 Discontinued
0.59 Remote Similarity NPD9605 Phase 3
0.5895 Remote Similarity NPD194 Clinical (unspecified phase)
0.5892 Remote Similarity NPD9408 Phase 3
0.5885 Remote Similarity NPD1808 Phase 1
0.588 Remote Similarity NPD4896 Clinical (unspecified phase)
0.5853 Remote Similarity NPD1063 Phase 2
0.5846 Remote Similarity NPD582 Approved
0.5833 Remote Similarity NPD5458 Discontinued
0.5821 Remote Similarity NPD231 Clinical (unspecified phase)
0.5815 Remote Similarity NPD4715 Clinical (unspecified phase)
0.5815 Remote Similarity NPD4714 Approved
0.5815 Remote Similarity NPD4713 Clinical (unspecified phase)
0.5815 Remote Similarity NPD34 Approved
0.5801 Remote Similarity NPD5072 Discontinued
0.5798 Remote Similarity NPD6036 Suspended
0.5791 Remote Similarity NPD8421 Discontinued
0.5781 Remote Similarity NPD1121 Approved
0.5781 Remote Similarity NPD1120 Approved
0.5758 Remote Similarity NPD1730 Discontinued
0.5756 Remote Similarity NPD6381 Phase 2
0.5755 Remote Similarity NPD7502 Clinical (unspecified phase)
0.5754 Remote Similarity NPD6351 Discovery
0.5749 Remote Similarity NPD2593 Clinical (unspecified phase)
0.5744 Remote Similarity NPD1571 Phase 2
0.5739 Remote Similarity NPD2450 Phase 2
0.5739 Remote Similarity NPD2452 Phase 2
0.5739 Remote Similarity NPD2453 Phase 2
0.5739 Remote Similarity NPD2451 Phase 2
0.5737 Remote Similarity NPD7486 Phase 1
0.5726 Remote Similarity NPD5887 Clinical (unspecified phase)
0.572 Remote Similarity NPD8271 Discontinued
0.5697 Remote Similarity NPD7197 Approved
0.5691 Remote Similarity NPD8329 Phase 3
0.5673 Remote Similarity NPD8119 Discontinued
0.5673 Remote Similarity NPD1572 Phase 2
0.5664 Remote Similarity NPD8370 Discontinued
0.5654 Remote Similarity NPD8326 Phase 3
0.5654 Remote Similarity NPD8327 Clinical (unspecified phase)
0.5654 Remote Similarity NPD8325 Phase 3
0.5652 Remote Similarity NPD5321 Phase 3
0.5652 Remote Similarity NPD7103 Approved
0.565 Remote Similarity NPD4950 Approved
0.5635 Remote Similarity NPD2253 Discontinued
0.5634 Remote Similarity NPD7198 Clinical (unspecified phase)
0.5622 Remote Similarity NPD4938 Phase 2
0.5616 Remote Similarity NPD353 Discontinued
0.5614 Remote Similarity NPD4599 Clinical (unspecified phase)
0.56 Remote Similarity NPD6992 Phase 2

  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