FAIRMol

Z426369012

Pose ID 8687 Compound 855 Pose 557

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 Z426369012
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
32.0 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.79, Jaccard 0.65, H-bond role recall 0.29
Burial
74%
Hydrophobic fit
84%
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.885 kcal/mol/HA) ✓ Good fit quality (FQ -8.45) ✓ Good H-bonds (4 bonds) ✓ Deep burial (74% SASA buried) ✓ Lipophilic contacts well-matched (84%) ✗ Very high strain energy (32.0 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (10)
Score
-25.668
kcal/mol
LE
-0.885
kcal/mol/HA
Fit Quality
-8.45
FQ (Leeson)
HAC
29
heavy atoms
MW
405
Da
LogP
4.40
cLogP
Final rank
3.2522
rank score
Inter norm
-0.981
normalised
Contacts
19
H-bonds 4
Strain ΔE
32.0 kcal/mol
SASA buried
74%
Lipo contact
84% BSA apolar/total
SASA unbound
665 Ų
Apolar buried
415 Ų

Interaction summary

HBD 1 HBA 3 HY 4 PI 3 CLASH 2

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 3.

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
Jaccard0.65RMSD-
HB strict3Strict recall0.33
HB same residue+role2HB role recall0.29
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
550 0.7089563717843353 -1.16107 -32.7603 7 17 0 0.00 0.00 - no Open
574 1.563273033931963 -0.894916 -24.9454 11 16 0 0.00 0.00 - no Open
570 1.8983530217649327 -0.895592 -25.6438 4 17 0 0.00 0.00 - no Open
540 2.188469065975241 -1.0946 -32.4734 8 16 0 0.00 0.00 - no Open
551 2.207343591774533 -0.891831 -26.4179 4 16 0 0.00 0.00 - no Open
552 2.6137459609030174 -0.787817 -13.6074 6 13 0 0.00 0.00 - no Open
549 2.8587233897033926 -0.913163 -23.9116 13 18 0 0.00 0.00 - no Open
575 3.0497306452736783 -0.876647 -24.2283 4 18 1 0.05 0.00 - no Open
579 3.14401003598703 -0.81951 -20.0537 7 14 0 0.00 0.00 - no Open
557 3.2521974787035832 -0.981282 -25.668 4 19 15 0.79 0.29 - no Current
564 3.7549715815477414 -1.09269 -33.0977 16 20 0 0.00 0.00 - no Open
549 4.546760674497128 -1.06745 -31.929 6 19 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 -25.668kcal/mol
Ligand efficiency (LE) -0.8851kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.449
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 29HA

Physicochemical properties
Molecular weight 405.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.40
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 32.01kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 137.47kcal/mol
Minimised FF energy 105.45kcal/mol

SASA & burial

✓ computed
SASA (unbound) 665.5Ų
Total solvent-accessible surface area of free ligand
BSA total 492.7Ų
Buried surface area upon binding
BSA apolar 414.8Ų
Hydrophobic contacts buried
BSA polar 77.9Ų
Polar contacts buried
Fraction buried 74.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 84.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2607.2Ų
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 1393.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)