FAIRMol

KB_HAT_176

Pose ID 4169 Compound 593 Pose 106

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
T07
T. brucei PTR1 T. brucei
Ligand KB_HAT_176
PDB6RX6↗

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
30.6 kcal/mol
Protein clashes
1
Internal clashes
3
Native overlap
contact recall 0.74, Jaccard 0.58, H-bond role recall 0.00
Burial
84%
Hydrophobic fit
81%
Reason: no major geometry red flags detected
1 protein-contact clashes 3 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.421 kcal/mol/HA) ✓ Good fit quality (FQ -13.97) ✓ Deep burial (84% SASA buried) ✓ Lipophilic contacts well-matched (81%) ✗ Very high strain energy (30.6 kcal/mol) ✗ Geometry warnings ✗ Minor protein-contact clashes (4) ✗ Many internal clashes (14)
Score
-45.474
kcal/mol
LE
-1.421
kcal/mol/HA
Fit Quality
-13.97
FQ (Leeson)
HAC
32
heavy atoms
MW
473
Da
LogP
3.29
cLogP
Strain ΔE
30.6 kcal/mol
SASA buried
84%
Lipo contact
81% BSA apolar/total
SASA unbound
706 Ų
Apolar buried
483 Ų

Interaction summary

HB 2 HY 24 PI 5 CLASH 3

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
Final rank1.341Score-45.474
Inter norm-0.962Intra norm-0.459
Top1000noExcludedno
Contacts19H-bonds2
Artifact reasongeometry warning; 14 clashes; 4 protein contact clashes; 2 cofactor-context clashes; high strain Δ 30.6
Residues
ARG14 CYS168 GLY205 LEU208 LEU209 LEU263 LYS220 MET163 MET169 MET213 NAP301 PHE171 PHE97 PRO210 SER207 TRP221 TYR174 VAL206 HIS267

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
NameTbPTR1_cW_6RX6_ReadyContacts19
PoseOpen native poseHB0
IFP residues
ARG14 ASP161 CYS168 GLY205 LEU208 LEU209 LYS178 MET213 NAP301 PHE171 PHE97 PRO210 PRO99 SER207 SER95 TRP221 TYR174 TYR98 VAL206
Current overlap14Native recall0.74
Jaccard0.58RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue0HB residue recall0.00

Protein summary

275 residues
Protein targetT07Atoms3932
Residues275Chains3
Residue summaryLEU:437; VAL:433; ALA:361; ARG:288; ILE:266; GLU:210; LYS:198; SER:198; ASN:182; THR:154; GLN:153; PHE:140; PRO:140; TYR:126; GLY:112; HIS:103

Receptor context

1 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 1 Excluded HETATM 0
Kept cofactors / ions
A:NAP301

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
106 1.3407220211642157 -0.961998 -45.4744 2 19 14 0.74 0.00 - no Current
100 2.5897002349762537 -0.793386 -44.8002 7 19 0 0.00 0.00 - no Open
141 3.579369288789724 -0.845161 -50.681 5 17 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 -45.474kcal/mol
Ligand efficiency (LE) -1.4211kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -13.975
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 32HA

Physicochemical properties
Molecular weight 473.0Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.29
Lipinski: ≤ 5
Rotatable bonds 10

Conformational strain (MMFF94s)
Strain energy (ΔE) 30.59kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 69.36kcal/mol
Minimised FF energy 38.77kcal/mol

SASA & burial

✓ computed
SASA (unbound) 706.5Ų
Total solvent-accessible surface area of free ligand
BSA total 594.5Ų
Buried surface area upon binding
BSA apolar 482.9Ų
Hydrophobic contacts buried
BSA polar 111.5Ų
Polar contacts buried
Fraction buried 84.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 81.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1719.0Ų
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 2051.9Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 906.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)