FAIRMol

NMT-TY0563

Pose ID 8380 Compound 937 Pose 250

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-TY0563
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
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
24.4 kcal/mol
Protein clashes
6
Internal clashes
6
Native overlap
contact recall 0.63, Jaccard 0.55, H-bond role recall 0.57
Burial
78%
Hydrophobic fit
52%
Reason: 6 internal clashes
6 protein-contact clashes 6 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.204 kcal/mol/HA) ✓ Good fit quality (FQ -10.63) ✓ Strong H-bond network (7 bonds) ✓ Deep burial (78% SASA buried) ✗ High strain energy (24.4 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (9)
Score
-27.696
kcal/mol
LE
-1.204
kcal/mol/HA
Fit Quality
-10.63
FQ (Leeson)
HAC
23
heavy atoms
MW
355
Da
LogP
0.77
cLogP
Final rank
4.7604
rank score
Inter norm
-1.225
normalised
Contacts
15
H-bonds 12
Strain ΔE
24.4 kcal/mol
SASA buried
78%
Lipo contact
52% BSA apolar/total
SASA unbound
544 Ų
Apolar buried
220 Ų

Interaction summary

HBD 2 HBA 5 HY 1 PI 3 CLASH 6

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 overlap12Native recall0.63
Jaccard0.55RMSD-
HB strict3Strict recall0.33
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
287 2.281771617029549 -1.06786 -23.7408 5 18 0 0.00 0.00 - no Open
343 2.4562087162844173 -1.10761 -25.4402 13 17 0 0.00 0.00 - no Open
304 2.461814278287188 -0.94473 -20.9121 7 12 0 0.00 0.00 - no Open
407 2.5036253322923585 -1.19433 -22.7362 8 16 0 0.00 0.00 - no Open
266 2.5178884740350864 -1.23759 -27.3191 9 14 0 0.00 0.00 - no Open
309 3.0017361607070128 -1.11231 -22.3337 10 15 0 0.00 0.00 - no Open
328 3.3135670361627176 -0.980585 -18.4335 10 16 0 0.00 0.00 - no Open
250 4.760381988626865 -1.22455 -27.6963 12 15 12 0.63 0.57 - no Current
275 5.006226701203945 -1.35207 -29.9759 16 19 0 0.00 0.00 - 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 -27.696kcal/mol
Ligand efficiency (LE) -1.2042kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.628
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 23HA

Physicochemical properties
Molecular weight 355.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 0.77
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 24.41kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -109.66kcal/mol
Minimised FF energy -134.06kcal/mol

SASA & burial

✓ computed
SASA (unbound) 543.7Ų
Total solvent-accessible surface area of free ligand
BSA total 422.2Ų
Buried surface area upon binding
BSA apolar 219.6Ų
Hydrophobic contacts buried
BSA polar 202.7Ų
Polar contacts buried
Fraction buried 77.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 52.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2403.7Ų
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 1378.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)