FAIRMol

TC249

Pose ID 8282 Compound 3654 Pose 152

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 TC249
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
12.6 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.74, Jaccard 0.67, H-bond role recall 0.57
Burial
79%
Hydrophobic fit
83%
Reason: no major geometry red flags detected
1 protein-contact clashes 44% of hydrophobic surface appears solvent-exposed (7/16 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.105 kcal/mol/HA) ✓ Good fit quality (FQ -9.59) ✓ Strong H-bond network (6 bonds) ✓ Deep burial (79% SASA buried) ✓ Lipophilic contacts well-matched (83%) ✗ Moderate strain (12.6 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (9)
Score
-24.299
kcal/mol
LE
-1.105
kcal/mol/HA
Fit Quality
-9.59
FQ (Leeson)
HAC
22
heavy atoms
MW
297
Da
LogP
1.72
cLogP
Final rank
3.6620
rank score
Inter norm
-1.255
normalised
Contacts
16
H-bonds 9
Strain ΔE
12.6 kcal/mol
SASA buried
79%
Lipo contact
83% BSA apolar/total
SASA unbound
553 Ų
Apolar buried
363 Ų

Interaction summary

HBD 2 HBA 4 HY 2 PI 1 CLASH 1

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. 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: 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
Jaccard0.67RMSD-
HB strict5Strict recall0.56
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
209 1.658167985971869 -1.08099 -22.5789 6 14 0 0.00 0.00 - no Open
152 3.6619829451586017 -1.25544 -24.2995 9 16 14 0.74 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 -24.299kcal/mol
Ligand efficiency (LE) -1.1045kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.589
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 22HA

Physicochemical properties
Molecular weight 297.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) 1.72
Lipinski: ≤ 5
Rotatable bonds 4

Conformational strain (MMFF94s)
Strain energy (ΔE) 12.61kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 139.41kcal/mol
Minimised FF energy 126.80kcal/mol

SASA & burial

✓ computed
SASA (unbound) 553.4Ų
Total solvent-accessible surface area of free ligand
BSA total 436.7Ų
Buried surface area upon binding
BSA apolar 363.3Ų
Hydrophobic contacts buried
BSA polar 73.4Ų
Polar contacts buried
Fraction buried 78.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 83.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2534.1Ų
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 1388.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)