FAIRMol

KB_HAT_128

Pose ID 10960 Compound 2858 Pose 117

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 KB_HAT_128
PDB5S9T↗

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 but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
19.9 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.67, Jaccard 0.38, H-bond role recall 0.00
Burial
83%
Hydrophobic fit
82%
Reason: 1 severe internal clashes
1 severe internal clashes 4 protein-contact clashes 4 intramolecular clashes
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.000 kcal/mol/HA) ✓ Good fit quality (FQ -8.53) ✓ Good H-bonds (5 bonds) ✓ Deep burial (83% SASA buried) ✓ Lipophilic contacts well-matched (82%) ✗ Moderate strain (19.9 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (8)
Score
-21.001
kcal/mol
LE
-1.000
kcal/mol/HA
Fit Quality
-8.53
FQ (Leeson)
HAC
21
heavy atoms
MW
300
Da
LogP
2.21
cLogP
Strain ΔE
19.9 kcal/mol
SASA buried
83%
Lipo contact
82% BSA apolar/total
SASA unbound
553 Ų
Apolar buried
376 Ų

Interaction summary

HB 5 HY 22 PI 3 CLASH 4 Severe 1
Final rank3.029Score-21.001
Inter norm-1.063Intra norm0.063
Top1000noExcludedno
Contacts17H-bonds5
Artifact reasongeometry warning; 8 clashes; 2 protein clashes; 1 cofactor-context clash
Residues
ALA363 ALA365 ARG228 FAD501 GLY196 GLY197 LEU227 LEU332 LEU334 PHE198 PHE230 PHE367 PRO336 SER364 VAL366 HIS461 VAL460

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
Jaccard0.38RMSD-
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
91 1.0974691656403437 -1.32703 -23.9273 5 15 0 0.00 0.00 - no Open
95 1.1145258582921873 -1.62284 -32.1529 8 18 0 0.00 0.00 - no Open
102 1.5423835052535655 -1.48174 -29.6335 5 13 0 0.00 0.00 - no Open
117 3.0289936264421713 -1.06315 -21.0006 5 17 8 0.67 0.00 - 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 -21.001kcal/mol
Ligand efficiency (LE) -1.0000kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.530
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 21HA

Physicochemical properties
Molecular weight 300.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.21
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 19.93kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -36.25kcal/mol
Minimised FF energy -56.18kcal/mol

SASA & burial

✓ computed
SASA (unbound) 553.2Ų
Total solvent-accessible surface area of free ligand
BSA total 459.4Ų
Buried surface area upon binding
BSA apolar 375.7Ų
Hydrophobic contacts buried
BSA polar 83.7Ų
Polar contacts buried
Fraction buried 83.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 81.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -6472.6Ų
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 8063.1Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 2051.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)