FAIRMol

Z1269163651

Pose ID 8792 Compound 2025 Pose 662

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 Z1269163651
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 high Native strong SASA done
Strain ΔE
28.8 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.79, Jaccard 0.71, H-bond role recall 0.43
Burial
85%
Hydrophobic fit
68%
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-2.178 kcal/mol/HA) ✓ Good fit quality (FQ -15.57) ✓ Strong H-bond network (12 bonds) ✓ Deep burial (85% SASA buried) ✓ Lipophilic contacts well-matched (68%) ✗ High strain energy (28.8 kcal/mol) ✗ Geometry warnings
Score
-30.485
kcal/mol
LE
-2.178
kcal/mol/HA
Fit Quality
-15.57
FQ (Leeson)
HAC
14
heavy atoms
MW
208
Da
LogP
-4.68
cLogP
Strain ΔE
28.8 kcal/mol
SASA buried
85%
Lipo contact
68% BSA apolar/total
SASA unbound
387 Ų
Apolar buried
224 Ų

Interaction summary

HB 12 HY 3 PI 0 CLASH 1

HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.

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

HY · Hydrophobic contacts

CLASH · Clashes
Final rank2.482Score-30.485
Inter norm-2.239Intra norm0.062
Top1000noExcludedno
Contacts17H-bonds12
Artifact reasongeometry warning; 1 clash; 3 protein clashes; moderate strain Δ 28.8
Residues
ALA67 ARG277 ASP88 CYS70 GLU274 GLY199 GLY235 GLY236 GLY237 GLY276 HIS197 LYS69 PHE238 PRO275 SER200 TYR278 TYR389

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
Jaccard0.71RMSD-
HB strict5Strict recall0.56
HB same residue+role3HB role recall0.43
HB same residue5HB residue recall0.71

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
657 1.3070008823646198 -2.31148 -29.4997 14 8 0 0.00 0.00 - no Open
662 2.481543155138736 -2.23948 -30.4848 12 17 15 0.79 0.43 - no Current
648 2.7801507953753766 -1.734 -24.3155 11 12 0 0.00 0.00 - no Open
660 2.9632763288987976 -1.63935 -23.3336 11 14 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 -30.485kcal/mol
Ligand efficiency (LE) -2.1775kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -15.569
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 14HA

Physicochemical properties
Molecular weight 208.2Da
Lipinski: ≤ 500 Da
LogP (cLogP) -4.68
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 28.80kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 146.08kcal/mol
Minimised FF energy 117.28kcal/mol

SASA & burial

✓ computed
SASA (unbound) 386.7Ų
Total solvent-accessible surface area of free ligand
BSA total 329.2Ų
Buried surface area upon binding
BSA apolar 223.6Ų
Hydrophobic contacts buried
BSA polar 105.6Ų
Polar contacts buried
Fraction buried 85.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 67.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2348.5Ų
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 1380.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)