FAIRMol

NMT-TY0435

Pose ID 8366 Compound 2529 Pose 236

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-TY0435
PDB1F3T↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak SASA cached
Weak or marginal quality
Binding strong Geometry medium Native strong SASA done
Strain ΔE
34.0 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.89, Jaccard 0.65, H-bond role recall 0.71
Burial
87%
Hydrophobic fit
75%
Reason: no major geometry red flags detected
5 protein-contact clashes 5 intramolecular clashes
EcoTox / ADMET In-silico prediction only
Fish LC₅₀
Cat. 3 — Harmful (10–100 mg/L)
Daphnia EC₅₀
Cat. 3 — Harmful (10–100 mg/L)
Algae IC₅₀
Cat. 3 — Harmful (10–100 mg/L)
Bioaccum.
Not B (BCF≤2000)
Persistent
No
ADMET alerts (in-silico)
hERG Medium Ames Clear DILI Low
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.161 kcal/mol/HA) ✓ Good fit quality (FQ -10.83) ✓ Strong H-bond network (10 bonds) ✓ Deep burial (87% SASA buried) ✓ Lipophilic contacts well-matched (75%) ✗ Very high strain energy (34.0 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (12)
Score
-31.342
kcal/mol
LE
-1.161
kcal/mol/HA
Fit Quality
-10.83
FQ (Leeson)
HAC
27
heavy atoms
MW
384
Da
LogP
3.03
cLogP
Final rank
5.2876
rank score
Inter norm
-1.348
normalised
Contacts
24
H-bonds 13
Strain ΔE
34.0 kcal/mol
SASA buried
87%
Lipo contact
75% BSA apolar/total
SASA unbound
634 Ų
Apolar buried
414 Ų

Interaction summary

HBD 2 HBA 8 HY 5 PI 3 CLASH 5

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 7.

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: strict.
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 overlap17Native recall0.89
Jaccard0.65RMSD-
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
280 1.3897600186198402 -0.883548 -15.2887 3 17 0 0.00 0.00 - no Open
278 2.7192167591062755 -0.878405 -21.2281 4 16 0 0.00 0.00 - no Open
266 4.658311657491511 -1.21611 -23.2432 13 15 0 0.00 0.00 - no Open
236 5.287574351639099 -1.34818 -31.3423 13 24 17 0.89 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 -31.342kcal/mol
Ligand efficiency (LE) -1.1608kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.830
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 27HA

Physicochemical properties
Molecular weight 384.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.03
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 34.03kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -178.72kcal/mol
Minimised FF energy -212.75kcal/mol

SASA & burial

✓ computed
SASA (unbound) 633.6Ų
Total solvent-accessible surface area of free ligand
BSA total 550.9Ų
Buried surface area upon binding
BSA apolar 413.8Ų
Hydrophobic contacts buried
BSA polar 137.0Ų
Polar contacts buried
Fraction buried 86.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 75.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2564.5Ų
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 1384.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)