FAIRMol

NMT-TY0819

Pose ID 8417 Compound 3760 Pose 287

DB SELECTIONDocking 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-TY0819
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
34.9 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.79, Jaccard 0.75, H-bond role recall 0.57
Burial
79%
Hydrophobic fit
65%
Reason: no major geometry red flags detected
4 protein-contact clashes 4 intramolecular clashes
EcoTox / ADMET GDS: SAFE UL GreenDrugScore ML model
ECOscore
0.957
aquatic tox · BCF · biodeg.
GDS₃ (3-block)
0.641
ADMET + ECO + DL
ADMETscore (GDS)
0.637
absorption · distr. · metab.
DLscore
0.461
drug-likeness
P(SAFE)
0.56
GDS classification
ADMET alerts (in-silico)
hERG Low Ames Clear DILI Low
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.904 kcal/mol/HA) ✓ Good fit quality (FQ -8.10) ✓ Strong H-bond network (9 bonds) ✓ Deep burial (79% SASA buried) ✓ Lipophilic contacts well-matched (65%) ✗ Very high strain energy (34.9 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (11)
Score
-21.703
kcal/mol
LE
-0.904
kcal/mol/HA
Fit Quality
-8.10
FQ (Leeson)
HAC
24
heavy atoms
MW
352
Da
LogP
-0.16
cLogP
Final rank
5.3301
rank score
Inter norm
-1.148
normalised
Contacts
16
H-bonds 12
Strain ΔE
34.9 kcal/mol
SASA buried
79%
Lipo contact
65% BSA apolar/total
SASA unbound
556 Ų
Apolar buried
285 Ų

Interaction summary

HBD 2 HBA 7 HY 3 PI 3 CLASH 4

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. 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: 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 overlap15Native recall0.79
Jaccard0.75RMSD-
HB strict6Strict recall0.67
HB same residue+role4HB role recall0.57
HB same residue4HB residue recall0.57

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
317 3.1304277591353276 -0.993049 -20.3489 4 13 0 0.00 0.00 - no Open
358 4.436950517901971 -0.948165 -22.5924 11 16 0 0.00 0.00 - no Open
287 5.330058749582769 -1.14795 -21.7031 12 16 15 0.79 0.57 - 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 -21.703kcal/mol
Ligand efficiency (LE) -0.9043kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.104
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 24HA

Physicochemical properties
Molecular weight 352.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) -0.16
Lipinski: ≤ 5
Rotatable bonds 4

Conformational strain (MMFF94s)
Strain energy (ΔE) 34.89kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -87.56kcal/mol
Minimised FF energy -122.45kcal/mol

SASA & burial

✓ computed
SASA (unbound) 555.7Ų
Total solvent-accessible surface area of free ligand
BSA total 438.0Ų
Buried surface area upon binding
BSA apolar 285.1Ų
Hydrophobic contacts buried
BSA polar 153.0Ų
Polar contacts buried
Fraction buried 78.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 65.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2448.6Ų
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 1378.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)