FAIRMol

Z45614013

Pose ID 8573 Compound 3245 Pose 443

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 Z45614013
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 medium Native strong SASA done
Strain ΔE
16.0 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.79, Jaccard 0.60, H-bond role recall 0.43
Burial
93%
Hydrophobic fit
69%
Reason: no major geometry red flags detected
3 protein-contact clashes 3 intramolecular clashes
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.702 kcal/mol/HA) ✓ Good fit quality (FQ -14.24) ✓ Strong H-bond network (7 bonds) ✓ Deep burial (93% SASA buried) ✓ Lipophilic contacts well-matched (69%) ✗ Moderate strain (16.0 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (7)
Score
-34.035
kcal/mol
LE
-1.702
kcal/mol/HA
Fit Quality
-14.24
FQ (Leeson)
HAC
20
heavy atoms
MW
312
Da
LogP
1.13
cLogP
Final rank
3.6987
rank score
Inter norm
-1.815
normalised
Contacts
21
H-bonds 8
Strain ΔE
16.0 kcal/mol
SASA buried
93%
Lipo contact
69% BSA apolar/total
SASA unbound
514 Ų
Apolar buried
329 Ų

Interaction summary

HBD 2 HBA 5 HY 5 PI 2 CLASH 3

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

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
Jaccard0.60RMSD-
HB strict5Strict recall0.56
HB same residue+role3HB role recall0.43
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
463 1.849767598748503 -1.26027 -22.944 9 14 0 0.00 0.00 - no Open
472 2.798095488823452 -1.286 -24.6828 11 15 0 0.00 0.00 - no Open
445 2.8871749129701585 -1.33197 -25.8246 5 14 0 0.00 0.00 - no Open
501 3.1689469733012934 -1.12908 -21.6016 7 15 1 0.05 0.00 - no Open
443 3.6986528364012434 -1.81516 -34.0355 8 21 15 0.79 0.43 - 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 -34.035kcal/mol
Ligand efficiency (LE) -1.7018kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -14.241
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 20HA

Physicochemical properties
Molecular weight 312.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 1.13
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 16.02kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -109.03kcal/mol
Minimised FF energy -125.05kcal/mol

SASA & burial

✓ computed
SASA (unbound) 513.9Ų
Total solvent-accessible surface area of free ligand
BSA total 479.4Ų
Buried surface area upon binding
BSA apolar 329.5Ų
Hydrophobic contacts buried
BSA polar 149.9Ų
Polar contacts buried
Fraction buried 93.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 68.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2430.6Ų
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 1377.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)