FAIRMol

NMT-TY0134

Pose ID 8344 Compound 4008 Pose 214

DB fairmolDocking pose analysis is being read from this database.
Compound detail Protein structures Back to compounds
Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
T13
T. brucei ODC (Active site) T. brucei Active site
Ligand NMT-TY0134
PDB1F3T↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Promising SASA cached
Promising and worth follow-up
Binding strong Geometry high Native strong SASA done
Strain ΔE
13.7 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.74, Jaccard 0.70, H-bond role recall 0.71
Burial
79%
Hydrophobic fit
46%
Reason: no major geometry red flags detected
1 protein-contact clashes
EcoTox / ADMET In-silico prediction only
Fish LC₅₀
Not classified (>100 mg/L)
Daphnia EC₅₀
Not classified (>100 mg/L)
Algae IC₅₀
Not classified (>100 mg/L)
Bioaccum.
Not B (BCF≤2000)
Persistent
No
ADMET alerts (in-silico)
hERG Low Ames Clear DILI Low
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.747 kcal/mol/HA) ✓ Good fit quality (FQ -12.91) ✓ Strong H-bond network (11 bonds) ✓ Deep burial (79% SASA buried) ✗ Moderate strain (13.7 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (6)
Score
-26.203
kcal/mol
LE
-1.747
kcal/mol/HA
Fit Quality
-12.91
FQ (Leeson)
HAC
15
heavy atoms
MW
228
Da
LogP
-0.14
cLogP
Final rank
3.2278
rank score
Inter norm
-1.870
normalised
Contacts
15
H-bonds 15
Strain ΔE
13.7 kcal/mol
SASA buried
79%
Lipo contact
46% BSA apolar/total
SASA unbound
380 Ų
Apolar buried
139 Ų

Interaction summary

HBD 2 HBA 9 HY 2 PI 2 CLASH 1

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 6.

PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.

HY · Hydrophobic contacts

CLASH · Clashes

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: permissive.
Name1F3TContacts19
PoseOpen native poseHB0
IFP residues
ALA111 ALA67 ARG154 ARG277 ASP332 ASP88 CYS70 GLU274 GLY236 GLY237 GLY276 HIS197 LYS69 PHE238 PRO275 SER200 TYR278 TYR331 TYR389
Current overlap14Native recall0.74
Jaccard0.70RMSD-
HB strict7Strict recall0.78
HB same residue+role5HB role recall0.71
HB same residue5HB residue recall0.71

Protein summary

411 residues
Protein targetT13Atoms6340
Residues411Chains1
Residue summaryVAL:624; LEU:551; LYS:506; ARG:480; PHE:460; ILE:418; ASP:348; GLU:332; THR:322; TYR:315; PRO:308; ALA:290; SER:264; GLY:224; ASN:210; GLN:170

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
214 3.227844332926758 -1.87025 -26.2027 15 15 14 0.74 0.71 - no Current

Molecular metrics

RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
✓ Metrics available

Scoring & efficiency
Docking score -26.203kcal/mol
Ligand efficiency (LE) -1.7468kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -12.908
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 15HA

Physicochemical properties
Molecular weight 228.2Da
Lipinski: ≤ 500 Da
LogP (cLogP) -0.14
Lipinski: ≤ 5
Rotatable bonds 4

Conformational strain (MMFF94s)
Strain energy (ΔE) 13.71kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -6.11kcal/mol
Minimised FF energy -19.82kcal/mol

SASA & burial

✓ computed
SASA (unbound) 380.1Ų
Total solvent-accessible surface area of free ligand
BSA total 301.7Ų
Buried surface area upon binding
BSA apolar 139.5Ų
Hydrophobic contacts buried
BSA polar 162.2Ų
Polar contacts buried
Fraction buried 79.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 46.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2277.2Ų
SASA_nonpolar(complex) − SASA_nonpolar(receptor) − SASA_nonpolar(ligand free). Negative = non-polar surface buried upon binding. Requires full polarity-decomposed SASA computation.
Receptor non-polar SASA 3461.2Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1377.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)