FAIRMol

TC552

Pose ID 8302 Compound 1888 Pose 172

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 TC552
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
13.2 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.58, Jaccard 0.44, H-bond role recall 0.43
Burial
81%
Hydrophobic fit
84%
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.972 kcal/mol/HA) ✓ Good fit quality (FQ -9.07) ✓ Strong H-bond network (6 bonds) ✓ Deep burial (81% SASA buried) ✓ Lipophilic contacts well-matched (84%) ✗ Moderate strain (13.2 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (8)
Score
-26.245
kcal/mol
LE
-0.972
kcal/mol/HA
Fit Quality
-9.07
FQ (Leeson)
HAC
27
heavy atoms
MW
367
Da
LogP
1.06
cLogP
Final rank
3.0439
rank score
Inter norm
-1.025
normalised
Contacts
17
H-bonds 10
Strain ΔE
13.2 kcal/mol
SASA buried
81%
Lipo contact
84% BSA apolar/total
SASA unbound
643 Ų
Apolar buried
437 Ų

Interaction summary

HBD 3 HBA 3 HY 3 PI 2 CLASH 2

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 4.

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 overlap11Native recall0.58
Jaccard0.44RMSD-
HB strict2Strict recall0.22
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
237 1.4290717238990738 -0.953072 -24.1167 1 20 0 0.00 0.00 - no Open
215 2.0171944907376305 -1.06213 -16.1562 7 17 0 0.00 0.00 - no Open
252 2.2051864699877384 -0.986889 -15.1919 5 13 0 0.00 0.00 - no Open
172 3.0439487765845445 -1.02531 -26.2453 10 17 11 0.58 0.43 - no Current
233 3.1278106641215495 -0.876137 -19.5221 8 16 0 0.00 0.00 - no Open
292 4.3181297952992415 -0.767501 -8.35862 6 8 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 -26.245kcal/mol
Ligand efficiency (LE) -0.9720kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.069
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 27HA

Physicochemical properties
Molecular weight 367.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 1.06
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 13.20kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 128.36kcal/mol
Minimised FF energy 115.16kcal/mol

SASA & burial

✓ computed
SASA (unbound) 643.4Ų
Total solvent-accessible surface area of free ligand
BSA total 518.9Ų
Buried surface area upon binding
BSA apolar 437.0Ų
Hydrophobic contacts buried
BSA polar 81.9Ų
Polar contacts buried
Fraction buried 80.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 84.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2579.7Ų
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 1406.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)