FAIRMol

NMT-TY0840

Pose ID 8418 Compound 3993 Pose 288

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-TY0840
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
10.7 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.79, Jaccard 0.79, H-bond role recall 0.43
Burial
93%
Hydrophobic fit
65%
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-2.063 kcal/mol/HA) ✓ Good fit quality (FQ -14.75) ✓ Strong H-bond network (7 bonds) ✓ Deep burial (93% SASA buried) ✓ Lipophilic contacts well-matched (65%) ✗ Moderate strain (10.7 kcal/mol) ✗ Geometry warnings
Score
-28.879
kcal/mol
LE
-2.063
kcal/mol/HA
Fit Quality
-14.75
FQ (Leeson)
HAC
14
heavy atoms
MW
214
Da
LogP
0.29
cLogP
Final rank
2.7291
rank score
Inter norm
-2.191
normalised
Contacts
15
H-bonds 7
Strain ΔE
10.7 kcal/mol
SASA buried
93%
Lipo contact
65% BSA apolar/total
SASA unbound
408 Ų
Apolar buried
246 Ų

Interaction summary

HBD 2 HBA 5 HY 4 PI 1 CLASH 1

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 5.

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 overlap15Native recall0.79
Jaccard0.79RMSD-
HB strict5Strict recall0.56
HB same residue+role3HB role recall0.43
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
288 2.729105136929018 -2.19061 -28.8793 7 15 15 0.79 0.43 - no Current
538 2.737273254576643 -2.1799 -28.6669 7 15 15 0.79 0.43 - no Open

Molecular metrics

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

Scoring & efficiency
Docking score -28.879kcal/mol
Ligand efficiency (LE) -2.0628kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -14.749
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 14HA

Physicochemical properties
Molecular weight 214.2Da
Lipinski: ≤ 500 Da
LogP (cLogP) 0.29
Lipinski: ≤ 5
Rotatable bonds 3

Conformational strain (MMFF94s)
Strain energy (ΔE) 10.71kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -84.48kcal/mol
Minimised FF energy -95.19kcal/mol

SASA & burial

✓ computed
SASA (unbound) 408.4Ų
Total solvent-accessible surface area of free ligand
BSA total 379.5Ų
Buried surface area upon binding
BSA apolar 246.3Ų
Hydrophobic contacts buried
BSA polar 133.2Ų
Polar contacts buried
Fraction buried 92.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 64.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2350.8Ų
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 1378.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)