FAIRMol

Z49545335

Pose ID 8535 Compound 3853 Pose 405

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 Z49545335
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 medium Native strong SASA done
Strain ΔE
24.0 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.79, Jaccard 0.58, H-bond role recall 0.57
Burial
87%
Hydrophobic fit
74%
Reason: no major geometry red flags detected
4 protein-contact clashes 4 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.352 kcal/mol/HA) ✓ Good fit quality (FQ -11.74) ✓ Strong H-bond network (9 bonds) ✓ Deep burial (87% SASA buried) ✓ Lipophilic contacts well-matched (74%) ✗ High strain energy (24.0 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (6)
Score
-29.742
kcal/mol
LE
-1.352
kcal/mol/HA
Fit Quality
-11.74
FQ (Leeson)
HAC
22
heavy atoms
MW
295
Da
LogP
0.29
cLogP
Final rank
2.0988
rank score
Inter norm
-1.248
normalised
Contacts
22
H-bonds 13
Strain ΔE
24.0 kcal/mol
SASA buried
87%
Lipo contact
74% BSA apolar/total
SASA unbound
533 Ų
Apolar buried
343 Ų

Interaction summary

HBD 2 HBA 7 PC 1 HY 4 PI 3 CLASH 4

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 7.

PC · Polar contacts (possible, no H geometry)
HBD?/HBA? — heavy-atom distance only, H geometry unavailable. May be real H-bonds.

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 overlap15Native recall0.79
Jaccard0.58RMSD-
HB strict6Strict recall0.67
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
398 1.9190361257320792 -1.2191 -26.0971 11 19 0 0.00 0.00 - no Open
405 2.0987535247410727 -1.24782 -29.7421 13 22 15 0.79 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 -29.742kcal/mol
Ligand efficiency (LE) -1.3519kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -11.737
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 22HA

Physicochemical properties
Molecular weight 295.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) 0.29
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 23.95kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 103.51kcal/mol
Minimised FF energy 79.55kcal/mol

SASA & burial

✓ computed
SASA (unbound) 533.1Ų
Total solvent-accessible surface area of free ligand
BSA total 466.1Ų
Buried surface area upon binding
BSA apolar 342.8Ų
Hydrophobic contacts buried
BSA polar 123.4Ų
Polar contacts buried
Fraction buried 87.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 73.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2487.2Ų
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 1383.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)