FAIRMol

KB_HAT_25

Pose ID 10946 Compound 108 Pose 103

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_25
PDB5S9T↗

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
24.5 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.58, Jaccard 0.30, H-bond role recall 0.00
Burial
77%
Hydrophobic fit
71%
Reason: no major geometry red flags detected
3 protein-contact clashes 3 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.661 kcal/mol/HA) ✓ Good fit quality (FQ -6.62) ✓ Good H-bonds (5 bonds) ✓ Deep burial (77% SASA buried) ✓ Lipophilic contacts well-matched (71%) ✗ High strain energy (24.5 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (13)
Score
-22.482
kcal/mol
LE
-0.661
kcal/mol/HA
Fit Quality
-6.62
FQ (Leeson)
HAC
34
heavy atoms
MW
476
Da
LogP
2.21
cLogP
Strain ΔE
24.5 kcal/mol
SASA buried
77%
Lipo contact
71% BSA apolar/total
SASA unbound
766 Ų
Apolar buried
419 Ų

Interaction summary

HB 5 HY 15 PI 0 CLASH 3
Final rank4.726Score-22.482
Inter norm-0.762Intra norm0.100
Top1000noExcludedno
Contacts18H-bonds5
Artifact reasongeometry warning; 13 clashes; 3 protein clashes; moderate strain Δ 24.5
Residues
ARG228 ARG361 CYS375 GLY196 GLY197 GLY229 GLY376 HIS359 LEU227 LEU332 LEU377 PHE198 PHE230 SER364 THR360 THR374 TYR221 VAL362

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 overlap7Native recall0.58
Jaccard0.30RMSD-
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
No pi · π–π interactions detected for this pose.

HY · Hydrophobic contacts

CLASH · Clashes

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
116 0.9967124239667426 -0.835107 -24.9422 1 19 0 0.00 0.00 - no Open
145 1.3995751921199313 -0.88415 -27.5642 3 16 0 0.00 0.00 - no Open
182 1.4861130235883124 -0.855269 -26.7745 4 22 0 0.00 0.00 - no Open
140 1.615020829250697 -0.925503 -28.3157 6 17 0 0.00 0.00 - no Open
161 2.662027008092362 -0.751934 -23.4535 3 14 0 0.00 0.00 - no Open
149 3.0092960382301914 -0.757482 -21.0618 2 22 0 0.00 0.00 - no Open
117 3.133913752613804 -0.893126 -27.6382 10 20 0 0.00 0.00 - no Open
92 3.1897154297188073 -0.7343 -24.0617 7 15 0 0.00 0.00 - no Open
109 3.266242765469782 -0.81009 -22.6151 5 16 0 0.00 0.00 - no Open
95 3.6098926606982675 -0.795677 -23.8078 8 16 0 0.00 0.00 - no Open
150 3.6690791561020983 -0.768661 -24.4817 6 18 7 0.58 0.00 - no Open
91 3.8086261390469938 -0.740979 -20.0503 5 21 0 0.00 0.00 - no Open
124 4.692634237226219 -0.64544 -22.9491 7 15 0 0.00 0.00 - no Open
103 4.725842136853786 -0.76159 -22.4824 5 18 7 0.58 0.00 - no Current
118 4.790784883872673 -0.731769 -21.8142 8 17 0 0.00 0.00 - no Open
73 4.7962875837914805 -1.009 -30.2636 11 20 0 0.00 0.00 - no Open
46 5.044122438992116 -0.80531 -23.3978 7 15 0 0.00 0.00 - no Open
87 5.0598912182116695 -0.712441 -22.3133 4 21 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 -22.482kcal/mol
Ligand efficiency (LE) -0.6612kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.616
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 34HA

Physicochemical properties
Molecular weight 475.6Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.21
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 24.46kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 53.79kcal/mol
Minimised FF energy 29.33kcal/mol

SASA & burial

✓ computed
SASA (unbound) 766.3Ų
Total solvent-accessible surface area of free ligand
BSA total 592.3Ų
Buried surface area upon binding
BSA apolar 419.3Ų
Hydrophobic contacts buried
BSA polar 173.1Ų
Polar contacts buried
Fraction buried 77.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 70.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -6566.1Ų
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 2086.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)