FAIRMol

Z56864891

Pose ID 11475 Compound 1333 Pose 632

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
T17
T. brucei TR (Doorstop site) T. brucei Doorstop site
Ligand Z56864891
PDB5S9T↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
48.8 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.67, Jaccard 0.36, H-bond role recall 0.00
Burial
78%
Hydrophobic fit
82%
Reason: strain 48.8 kcal/mol
strain ΔE 48.8 kcal/mol 1 protein-contact clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.815 kcal/mol/HA) ✓ Good fit quality (FQ -8.16) ✓ Good H-bonds (4 bonds) ✓ Deep burial (78% SASA buried) ✓ Lipophilic contacts well-matched (82%) ✗ Extreme strain energy (48.8 kcal/mol) ✗ Geometry warnings ✗ Minor protein-contact clashes (2) ✗ Many internal clashes (15)
Score
-27.714
kcal/mol
LE
-0.815
kcal/mol/HA
Fit Quality
-8.16
FQ (Leeson)
HAC
34
heavy atoms
MW
522
Da
LogP
4.32
cLogP
Strain ΔE
48.8 kcal/mol
SASA buried
78%
Lipo contact
82% BSA apolar/total
SASA unbound
760 Ų
Apolar buried
484 Ų

Interaction summary

HB 4 HY 24 PI 3 CLASH 1
Final rank1.391Score-27.714
Inter norm-0.698Intra norm-0.117
Top1000noExcludedno
Contacts18H-bonds4
Artifact reasongeometry warning; 15 clashes; 2 protein contact clashes; high strain Δ 48.8
Residues
ALA284 ALA365 ARG228 ARG287 GLY196 GLY197 GLY286 ILE199 ILE285 LEU227 LEU332 LEU334 PHE198 PHE230 SER200 SER364 TYR221 VAL366

Protein summary

1033 residues
Protein targetT17Atoms15160
Residues1033Chains2
Residue summaryVAL:1536; LEU:1387; LYS:1386; ILE:1064; GLU:900; THR:868; ARG:816; PHE:800; ALA:780; ASN:700; PRO:686; GLY:672; SER:616; TYR:588; ASP:528; MET:408

Receptor context

2 kept / 0 excluded
Receptor context filtering: interactions and SASA are computed against protein atoms plus allowed cofactors/ions. Native ligand-like HETATM partners are excluded from scoring.
Kept context 2 Excluded HETATM 0
Kept cofactors / ions
A:FAD501 B:FAD501

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name5S9TContacts12
PoseOpen native poseHB0
IFP residues
ALA365 ARG228 ARG331 GLY229 LEU332 LEU334 MET333 PHE198 PHE230 SER364 THR374 VAL366
Current overlap8Native recall0.67
Jaccard0.36RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue0HB residue recall0.00

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

PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.

HY · Hydrophobic contacts

CLASH · Clashes

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
632 1.3905353742007591 -0.698084 -27.7143 4 18 8 0.67 0.00 - no Current
625 2.7569674706527576 -0.800866 -29.3178 3 17 0 0.00 0.00 - no Open
631 3.9861040146501385 -1.0328 -39.1984 10 22 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 -27.714kcal/mol
Ligand efficiency (LE) -0.8151kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.156
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 34HA

Physicochemical properties
Molecular weight 522.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.32
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 48.83kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 6.18kcal/mol
Minimised FF energy -42.64kcal/mol

SASA & burial

✓ computed
SASA (unbound) 759.7Ų
Total solvent-accessible surface area of free ligand
BSA total 590.2Ų
Buried surface area upon binding
BSA apolar 484.4Ų
Hydrophobic contacts buried
BSA polar 105.8Ų
Polar contacts buried
Fraction buried 77.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 82.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -6605.8Ų
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 8063.1Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 2070.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)