FAIRMol

NMT-TY0602

Pose ID 8388 Compound 643 Pose 258

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-TY0602
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
38.3 kcal/mol
Protein clashes
6
Internal clashes
6
Native overlap
contact recall 0.84, Jaccard 0.64, H-bond role recall 0.57
Burial
87%
Hydrophobic fit
58%
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 (-1.203 kcal/mol/HA) ✓ Good fit quality (FQ -10.78) ✓ Strong H-bond network (6 bonds) ✓ Deep burial (87% SASA buried) ✗ Very high strain energy (38.3 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (9)
Score
-28.866
kcal/mol
LE
-1.203
kcal/mol/HA
Fit Quality
-10.78
FQ (Leeson)
HAC
24
heavy atoms
MW
371
Da
LogP
0.32
cLogP
Final rank
4.0506
rank score
Inter norm
-1.183
normalised
Contacts
22
H-bonds 12
Strain ΔE
38.3 kcal/mol
SASA buried
87%
Lipo contact
58% BSA apolar/total
SASA unbound
556 Ų
Apolar buried
282 Ų

Interaction summary

HBD 2 HBA 4 PC 1 HY 4 PI 2 CLASH 6

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

PC · Polar contacts (possible, no H geometry)
HBD?/HBA? — heavy-atom distance only, H geometry unavailable. May be real H-bonds.

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 overlap16Native recall0.84
Jaccard0.64RMSD-
HB strict4Strict recall0.44
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
345 2.3852300086674956 -1.22883 -27.1471 9 14 0 0.00 0.00 - no Open
314 2.517801636797984 -0.942176 -24.1381 5 13 0 0.00 0.00 - no Open
272 2.9189537056135753 -1.1672 -29.7247 13 13 0 0.00 0.00 - no Open
414 3.1764200655621546 -1.06469 -24.8485 7 16 0 0.00 0.00 - no Open
297 3.248504433051989 -0.969391 -16.4093 6 17 0 0.00 0.00 - no Open
274 3.710791772393639 -1.07629 -24.7513 9 15 0 0.00 0.00 - no Open
383 3.8800478154472353 -1.20228 -28.5869 11 16 1 0.05 0.00 - no Open
258 4.050558324957515 -1.18293 -28.8656 12 22 16 0.84 0.57 - no Current
259 4.168971048980509 -1.13785 -26.3976 11 13 0 0.00 0.00 - no Open
364 4.531136784780454 -1.24281 -28.4071 7 15 0 0.00 0.00 - no Open
247 4.9387540833797265 -1.05098 -20.2639 12 13 0 0.00 0.00 - no Open
285 5.825536396152312 -1.3346 -31.8099 16 21 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 -28.866kcal/mol
Ligand efficiency (LE) -1.2027kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.779
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 24HA

Physicochemical properties
Molecular weight 371.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 0.32
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 38.29kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -45.02kcal/mol
Minimised FF energy -83.30kcal/mol

SASA & burial

✓ computed
SASA (unbound) 556.2Ų
Total solvent-accessible surface area of free ligand
BSA total 482.8Ų
Buried surface area upon binding
BSA apolar 281.7Ų
Hydrophobic contacts buried
BSA polar 201.0Ų
Polar contacts buried
Fraction buried 86.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 58.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2427.1Ų
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 1367.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)