FAIRMol

1F3T

Pose ID 8808

DB fairmolDocking pose analysis is being read from this database.
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 1F3T
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
Likely artefact or unreliable pose
Binding weak Geometry low Native strong SASA done
Strain ΔE
173.4 kcal/mol
Protein clashes
0
Internal clashes
0
Native overlap
contact recall 1.00, Jaccard 1.00, H-bond role recall 1.00
Burial
82%
Hydrophobic fit
65%
Reason: strain 173.4 kcal/mol
strain ΔE 173.4 kcal/mol 83% of hydrophobic surface is solvent-exposed (10/12 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Strong H-bond network (8 bonds) ✓ Deep burial (82% SASA buried) ✓ Lipophilic contacts well-matched (65%) ✗ Extreme strain energy (173.4 kcal/mol)
HAC
21
heavy atoms
MW
318
Da
LogP
0.11
cLogP
Contacts
19
H-bonds 10
Strain ΔE
173.4 kcal/mol
SASA buried
82%
Lipo contact
65% BSA apolar/total
SASA unbound
584 Ų
Apolar buried
308 Ų

Interaction summary

HBA 8 HY 2 PI 0 CLASH 0

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

PI · π–π interactions
No pi · π–π interactions detected for this pose.

HY · Hydrophobic contacts

CLASH · Clashes
No clash · clashes detected for this pose.

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 overlap19Native recall1.00
Jaccard1.00RMSD0.00 Å
HB strict9Strict recall1.00
HB same residue+role7HB role recall1.00
HB same residue7HB residue recall1.00

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
- ★ Native - - - 10 19 19 1.00 1.00 0.00 Å no Current

Molecular metrics

RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
✓ Metrics available

Scoring & efficiency
Heavy atom count 21HA

Physicochemical properties
Molecular weight 318.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) 0.11
Lipinski: ≤ 5
Rotatable bonds 10

Conformational strain (MMFF94s)
Strain energy (ΔE) 173.37kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -212.01kcal/mol
Minimised FF energy -385.38kcal/mol

SASA & burial

✓ computed
SASA (unbound) 583.5Ų
Total solvent-accessible surface area of free ligand
BSA total 476.9Ų
Buried surface area upon binding
BSA apolar 308.1Ų
Hydrophobic contacts buried
BSA polar 168.8Ų
Polar contacts buried
Fraction buried 81.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 64.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2507.0Ų
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 1360.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)