Structure

Physi-Chem Properties

Molecular Weight:  534.11
Volume:  484.299
LogP:  0.307
LogD:  -0.02
LogS:  -3.051
# Rotatable Bonds:  5
TPSA:  154.18
# H-Bond Aceptor:  10
# H-Bond Donor:  6
# Rings:  8
# Heavy Atoms:  12

MedChem Properties

QED Drug-Likeness Score:  0.233
Synthetic Accessibility Score:  7.503
Fsp3:  0.32
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:  -5.773
MDCK Permeability:  1.5080087223395822e-06
Pgp-inhibitor:  0.0
Pgp-substrate:  0.997
Human Intestinal Absorption (HIA):  0.961
20% Bioavailability (F20%):  0.957
30% Bioavailability (F30%):  0.985

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.309
Plasma Protein Binding (PPB):  72.25445556640625%
Volume Distribution (VD):  1.045
Pgp-substrate:  20.652151107788086%

ADMET: Metabolism

CYP1A2-inhibitor:  0.014
CYP1A2-substrate:  0.147
CYP2C19-inhibitor:  0.11
CYP2C19-substrate:  0.056
CYP2C9-inhibitor:  0.06
CYP2C9-substrate:  0.703
CYP2D6-inhibitor:  0.027
CYP2D6-substrate:  0.136
CYP3A4-inhibitor:  0.055
CYP3A4-substrate:  0.161

ADMET: Excretion

Clearance (CL):  2.81
Half-life (T1/2):  0.957

ADMET: Toxicity

hERG Blockers:  0.017
Human Hepatotoxicity (H-HT):  0.666
Drug-inuced Liver Injury (DILI):  0.882
AMES Toxicity:  0.121
Rat Oral Acute Toxicity:  0.652
Maximum Recommended Daily Dose:  0.917
Skin Sensitization:  0.224
Carcinogencity:  0.253
Eye Corrosion:  0.003
Eye Irritation:  0.006
Respiratory Toxicity:  0.805

Download Data

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

  Natural Product: NPC477417

Natural Product ID:  NPC477417
Common Name*:   Discorhabdin H
IUPAC Name:   n.a.
Synonyms:   Discorhabdin H
Standard InCHIKey:  ARYKGGHKIXVLJL-IBYWWYHMSA-P
Standard InCHI:  InChI=1S/C25H22N6O4S2/c1-30-8-28-23(11(30)4-10(26)24(34)35)37-22-19-12(32)5-13-25(22)6-14(36-13)29-18-16(25)20-15-9(2-3-31(19)20)7-27-17(15)21(18)33/h5,7-8,10,14,19,22H,2-4,6,26H2,1H3,(H2,27,29,33,34,35)/p+2/t10?,14-,19+,22-,25?/m0/s1
SMILES:  [H][C@]12C(=O)C=C3S[C@H]4CC3(C3=C(N4)C(=O)C4=C5C(=CN4)CC[N+]1=C53)[C@H]2SC1=C(CC([NH3+])C(=O)O)N(C)C=N1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   n.a.
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]

*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
NPO32733 latrunculia sp. Species Latrunculiidae Eukaryota n.a. Anita Bay, in Milford Sound, Fiordland, New Zealand, at a depth of ~22 m 2003-NOV PMID[16378380]
NPO32733 latrunculia sp. Species Latrunculiidae Eukaryota n.a. n.a. n.a. PMID[20337497]
NPO32733 latrunculia sp. Species Latrunculiidae Eukaryota n.a. New Zealand n.a. PMID[20860391]

☑ 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 > 8200 nM PMID[20860391]

☑ 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 NPC477417 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 NPC477419
0.7911 Intermediate Similarity NPC477420
0.7911 Intermediate Similarity NPC477418
0.625 Remote Similarity NPC477118
0.6239 Remote Similarity NPC476252
0.6238 Remote Similarity NPC60537
0.6233 Remote Similarity NPC476143
0.6221 Remote Similarity NPC469359
0.6221 Remote Similarity NPC477120
0.6162 Remote Similarity NPC327477
0.6154 Remote Similarity NPC286696
0.6121 Remote Similarity NPC477119
0.6094 Remote Similarity NPC476158
0.6087 Remote Similarity NPC469577
0.6087 Remote Similarity NPC475410
0.6071 Remote Similarity NPC185903
0.6059 Remote Similarity NPC477416
0.6045 Remote Similarity NPC477415
0.6045 Remote Similarity NPC474259
0.6045 Remote Similarity NPC23476
0.602 Remote Similarity NPC210947
0.6 Remote Similarity NPC469563
0.6 Remote Similarity NPC18223
0.6 Remote Similarity NPC237812
0.5992 Remote Similarity NPC238945
0.5991 Remote Similarity NPC71238
0.5991 Remote Similarity NPC469578
0.5983 Remote Similarity NPC54981
0.594 Remote Similarity NPC469562
0.594 Remote Similarity NPC220594
0.5938 Remote Similarity NPC313504
0.5911 Remote Similarity NPC477414
0.5911 Remote Similarity NPC225622
0.5911 Remote Similarity NPC221726
0.5897 Remote Similarity NPC126634
0.5843 Remote Similarity NPC314774
0.5843 Remote Similarity NPC315126
0.5837 Remote Similarity NPC323244
0.5825 Remote Similarity NPC25465
0.5796 Remote Similarity NPC201900
0.5787 Remote Similarity NPC143075
0.5781 Remote Similarity NPC324815
0.575 Remote Similarity NPC177996
0.575 Remote Similarity NPC147983
0.5748 Remote Similarity NPC39092
0.5744 Remote Similarity NPC235501
0.5744 Remote Similarity NPC470138
0.5743 Remote Similarity NPC328924
0.5742 Remote Similarity NPC472833
0.5735 Remote Similarity NPC18308
0.5735 Remote Similarity NPC124276
0.5735 Remote Similarity NPC472832
0.572 Remote Similarity NPC63279
0.5707 Remote Similarity NPC470140
0.57 Remote Similarity NPC470139
0.5697 Remote Similarity NPC297642
0.5693 Remote Similarity NPC8590
0.5686 Remote Similarity NPC295452
0.5686 Remote Similarity NPC171393
0.5663 Remote Similarity NPC69843
0.5662 Remote Similarity NPC477634
0.5654 Remote Similarity NPC116555
0.5639 Remote Similarity NPC268966
0.5602 Remote Similarity NPC282247
0.56 Remote Similarity NPC470141

  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 NPC477417 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
0.6897 Remote Similarity NPD3108 Clinical (unspecified phase)
0.6535 Remote Similarity NPD3130 Discontinued
0.6432 Remote Similarity NPD8261 Discontinued
0.6316 Remote Similarity NPD3105 Discontinued
0.6256 Remote Similarity NPD2604 Approved
0.6238 Remote Similarity NPD2180 Approved
0.6173 Remote Similarity NPD1451 Approved
0.6166 Remote Similarity NPD9628 Approved
0.6111 Remote Similarity NPD9627 Approved
0.6091 Remote Similarity NPD5935 Discontinued
0.6071 Remote Similarity NPD875 Clinical (unspecified phase)
0.6062 Remote Similarity NPD5461 Discontinued
0.6061 Remote Similarity NPD5342 Clinical (unspecified phase)
0.6034 Remote Similarity NPD6628 Discontinued
0.601 Remote Similarity NPD9183 Clinical (unspecified phase)
0.6009 Remote Similarity NPD3347 Clinical (unspecified phase)
0.6 Remote Similarity NPD9133 Approved
0.5992 Remote Similarity NPD8075 Discontinued
0.5984 Remote Similarity NPD2893 Phase 3
0.5983 Remote Similarity NPD3497 Clinical (unspecified phase)
0.5975 Remote Similarity NPD5046 Discontinued
0.5955 Remote Similarity NPD7245 Approved
0.5955 Remote Similarity NPD7246 Clinical (unspecified phase)
0.5949 Remote Similarity NPD576 Discontinued
0.5942 Remote Similarity NPD3697 Discontinued
0.5924 Remote Similarity NPD8271 Discontinued
0.5923 Remote Similarity NPD7981 Discontinued
0.5885 Remote Similarity NPD8641 Approved
0.588 Remote Similarity NPD7834 Approved
0.5874 Remote Similarity NPD1731 Clinical (unspecified phase)
0.5872 Remote Similarity NPD3966 Clinical (unspecified phase)
0.5837 Remote Similarity NPD3967 Approved
0.5829 Remote Similarity NPD5768 Phase 2
0.5826 Remote Similarity NPD6381 Phase 2
0.5821 Remote Similarity NPD3706 Clinical (unspecified phase)
0.5805 Remote Similarity NPD7465 Suspended
0.5792 Remote Similarity NPD5524 Approved
0.5792 Remote Similarity NPD5523 Approved
0.5787 Remote Similarity NPD2443 Approved
0.5787 Remote Similarity NPD2442 Approved
0.5779 Remote Similarity NPD6173 Approved
0.5772 Remote Similarity NPD8292 Phase 2
0.5763 Remote Similarity NPD3968 Approved
0.5763 Remote Similarity NPD2408 Discontinued
0.5755 Remote Similarity NPD5986 Approved
0.5755 Remote Similarity NPD5987 Approved
0.575 Remote Similarity NPD3353 Approved
0.5743 Remote Similarity NPD567 Approved
0.5743 Remote Similarity NPD566 Approved
0.5743 Remote Similarity NPD568 Approved
0.5743 Remote Similarity NPD8119 Discontinued
0.5734 Remote Similarity NPD3877 Approved
0.5732 Remote Similarity NPD5679 Clinical (unspecified phase)
0.5732 Remote Similarity NPD2847 Phase 2
0.5732 Remote Similarity NPD7557 Clinical (unspecified phase)
0.572 Remote Similarity NPD4960 Approved
0.572 Remote Similarity NPD4959 Approved
0.5714 Remote Similarity NPD3405 Phase 3
0.5714 Remote Similarity NPD4863 Approved
0.5708 Remote Similarity NPD3876 Approved
0.5702 Remote Similarity NPD2008 Discontinued
0.5701 Remote Similarity NPD717 Approved
0.5696 Remote Similarity NPD2880 Discontinued
0.5682 Remote Similarity NPD3041 Approved
0.5678 Remote Similarity NPD8410 Clinical (unspecified phase)
0.5678 Remote Similarity NPD3411 Phase 2
0.5678 Remote Similarity NPD3410 Approved
0.5672 Remote Similarity NPD4495 Phase 1
0.5665 Remote Similarity NPD5333 Clinical (unspecified phase)
0.5665 Remote Similarity NPD6837 Clinical (unspecified phase)
0.5647 Remote Similarity NPD5665 Clinical (unspecified phase)
0.5645 Remote Similarity NPD6165 Phase 2
0.5645 Remote Similarity NPD6164 Phase 2
0.5642 Remote Similarity NPD3333 Approved
0.5642 Remote Similarity NPD3332 Approved
0.5641 Remote Similarity NPD1807 Clinical (unspecified phase)
0.5633 Remote Similarity NPD460 Discontinued
0.563 Remote Similarity NPD6545 Clinical (unspecified phase)
0.5627 Remote Similarity NPD8484 Phase 2
0.5625 Remote Similarity NPD2411 Approved
0.5619 Remote Similarity NPD2009 Clinical (unspecified phase)
0.5612 Remote Similarity NPD4415 Approved
0.5608 Remote Similarity NPD7241 Phase 3
0.5608 Remote Similarity NPD7242 Phase 3
0.5603 Remote Similarity NPD3469 Phase 3
0.56 Remote Similarity NPD6092 Discontinued

  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