FAIRMol

TC391

Pose ID 8294 Compound 477 Pose 164

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 TC391
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 high Native strong SASA done
Strain ΔE
28.2 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.74, Jaccard 0.61, H-bond role recall 0.43
Burial
74%
Hydrophobic fit
83%
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.797 kcal/mol/HA) ✓ Good fit quality (FQ -7.69) ✓ Strong H-bond network (6 bonds) ✓ Deep burial (74% SASA buried) ✓ Lipophilic contacts well-matched (83%) ✗ High strain energy (28.2 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (15)
Score
-23.912
kcal/mol
LE
-0.797
kcal/mol/HA
Fit Quality
-7.69
FQ (Leeson)
HAC
30
heavy atoms
MW
428
Da
LogP
4.90
cLogP
Final rank
2.7801
rank score
Inter norm
-0.981
normalised
Contacts
18
H-bonds 8
Strain ΔE
28.2 kcal/mol
SASA buried
74%
Lipo contact
83% BSA apolar/total
SASA unbound
673 Ų
Apolar buried
416 Ų

Interaction summary

HBD 1 HBA 5 HY 3 PI 3 CLASH 1

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. 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: 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 overlap14Native recall0.74
Jaccard0.61RMSD-
HB strict3Strict recall0.33
HB same residue+role3HB role recall0.43
HB same residue3HB residue recall0.43

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
232 1.8331583620386547 -1.27971 -26.7454 4 18 0 0.00 0.00 - no Open
280 2.0200071560901884 -0.858313 -23.3297 3 18 0 0.00 0.00 - no Open
274 2.045457668570819 -0.972567 -23.9357 6 14 0 0.00 0.00 - no Open
166 2.6403647932585232 -0.945898 -27.3365 11 17 0 0.00 0.00 - no Open
252 2.7011556067534275 -0.828299 -17.981 8 15 0 0.00 0.00 - no Open
301 2.747981289497286 -0.894508 -23.189 4 18 0 0.00 0.00 - no Open
164 2.7801382971405904 -0.980978 -23.9123 8 18 14 0.74 0.43 - no Current
259 2.982627401034303 -0.855249 -21.6476 7 16 0 0.00 0.00 - no Open
365 3.608801145484245 -0.888327 -22.7927 5 16 0 0.00 0.00 - no Open
221 3.673195067444817 -1.01885 -23.2926 9 17 0 0.00 0.00 - no Open
198 3.840362266733292 -0.951165 -20.9586 6 18 0 0.00 0.00 - no Open
337 4.12591610565581 -0.761025 -21.4826 7 13 0 0.00 0.00 - no Open
183 4.337579311682156 -1.02771 -24.7008 7 20 0 0.00 0.00 - no Open
221 4.478220481332508 -1.00163 -22.7724 5 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 -23.912kcal/mol
Ligand efficiency (LE) -0.7971kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.689
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 30HA

Physicochemical properties
Molecular weight 427.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.90
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 28.23kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 82.30kcal/mol
Minimised FF energy 54.07kcal/mol

SASA & burial

✓ computed
SASA (unbound) 673.5Ų
Total solvent-accessible surface area of free ligand
BSA total 499.9Ų
Buried surface area upon binding
BSA apolar 416.0Ų
Hydrophobic contacts buried
BSA polar 83.8Ų
Polar contacts buried
Fraction buried 74.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 83.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2611.3Ų
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 1392.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)