FAIRMol

NMT-TY0943

Pose ID 8429 Compound 478 Pose 299

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-TY0943
PDB1F3T↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
65.4 kcal/mol
Protein clashes
11
Internal clashes
11
Native overlap
contact recall 0.84, Jaccard 0.62, H-bond role recall 0.57
Burial
84%
Hydrophobic fit
67%
Reason: 11 protein-contact clashes, 11 internal clashes, strain 65.4 kcal/mol
strain ΔE 65.4 kcal/mol 11 protein-contact clashes 11 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.767 kcal/mol/HA) ✓ Good fit quality (FQ -7.33) ✓ Strong H-bond network (8 bonds) ✓ Deep burial (84% SASA buried) ✓ Lipophilic contacts well-matched (67%) ✗ Extreme strain energy (65.4 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (13)
Score
-22.256
kcal/mol
LE
-0.767
kcal/mol/HA
Fit Quality
-7.33
FQ (Leeson)
HAC
29
heavy atoms
MW
434
Da
LogP
2.24
cLogP
Final rank
6.2646
rank score
Inter norm
-0.986
normalised
Contacts
23
H-bonds 10
Strain ΔE
65.4 kcal/mol
SASA buried
84%
Lipo contact
67% BSA apolar/total
SASA unbound
677 Ų
Apolar buried
383 Ų

Interaction summary

HBD 3 HBA 5 HY 4 PI 3 CLASH 11

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 overlap16Native recall0.84
Jaccard0.62RMSD-
HB strict5Strict recall0.56
HB same residue+role4HB role recall0.57
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
348 0.8052625623810137 -0.956826 -26.5786 1 13 0 0.00 0.00 - no Open
330 1.329263884816044 -0.859526 -24.8294 4 17 0 0.00 0.00 - no Open
326 2.453092962966273 -0.93103 -26.9955 10 12 0 0.00 0.00 - no Open
376 2.4975808499608676 -0.967058 -25.9968 4 17 0 0.00 0.00 - no Open
397 2.750322901945091 -1.0068 -27.2349 6 15 0 0.00 0.00 - no Open
286 2.8402209002504564 -1.18094 -33.1271 8 21 0 0.00 0.00 - no Open
340 3.0348573502876355 -0.845126 -25.451 13 14 0 0.00 0.00 - no Open
307 3.364737405609164 -1.16289 -34.6979 10 15 0 0.00 0.00 - no Open
383 3.6446324022786087 -0.978854 -27.1972 6 14 0 0.00 0.00 - no Open
372 4.744139486087101 -0.827695 -24.2166 8 20 0 0.00 0.00 - no Open
292 5.145683840208263 -1.07823 -23.7962 10 13 0 0.00 0.00 - no Open
299 6.264571217814828 -0.9861 -22.256 10 23 16 0.84 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 -22.256kcal/mol
Ligand efficiency (LE) -0.7674kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.326
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 29HA

Physicochemical properties
Molecular weight 434.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.24
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 65.43kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 12.48kcal/mol
Minimised FF energy -52.96kcal/mol

SASA & burial

✓ computed
SASA (unbound) 677.0Ų
Total solvent-accessible surface area of free ligand
BSA total 571.6Ų
Buried surface area upon binding
BSA apolar 383.0Ų
Hydrophobic contacts buried
BSA polar 188.6Ų
Polar contacts buried
Fraction buried 84.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 67.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2524.9Ų
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 1385.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)