FAIRMol

KB_Leish_184

Pose ID 4905 Compound 2905 Pose 164

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
T08
T. brucei PTR1 T. brucei
Ligand KB_Leish_184
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
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
11.6 kcal/mol
Protein clashes
4
Internal clashes
7
Native overlap
contact recall 0.79, Jaccard 0.71, H-bond role recall 0.60
Burial
98%
Hydrophobic fit
83%
Reason: 7 internal clashes
4 protein-contact clashes 7 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.327 kcal/mol/HA) ✓ Good fit quality (FQ -11.90) ✓ Good H-bonds (5 bonds) ✓ Deep burial (98% SASA buried) ✓ Lipophilic contacts well-matched (83%) ✗ Moderate strain (11.6 kcal/mol) ✗ Geometry warnings ✗ Protein-contact clashes (7) ✗ Many internal clashes (16)
Score
-31.858
kcal/mol
LE
-1.327
kcal/mol/HA
Fit Quality
-11.90
FQ (Leeson)
HAC
24
heavy atoms
MW
323
Da
LogP
1.11
cLogP
Final rank
1.5627
rank score
Inter norm
-1.402
normalised
Contacts
17
H-bonds 9
Strain ΔE
11.6 kcal/mol
SASA buried
98%
Lipo contact
83% BSA apolar/total
SASA unbound
541 Ų
Apolar buried
444 Ų

Interaction summary

HBD 5 HY 9 PI 2 CLASH 7

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 3.

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

HY · Hydrophobic contacts

CLASH · Clashes

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 overlap15Native recall0.79
Jaccard0.71RMSD-
HB strict4Strict recall0.67
HB same residue+role3HB role recall0.60
HB same residue3HB residue recall0.60

Protein summary

258 residues
Protein targetT08Atoms3881
Residues258Chains2
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
164 1.5626524427287396 -1.40194 -31.8585 9 17 15 0.79 0.60 - no Current
126 2.3916176710034507 -1.31279 -32.5369 11 16 12 0.63 0.60 - no Open
123 3.366640900721431 -1.21402 -29.7332 4 18 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 -31.858kcal/mol
Ligand efficiency (LE) -1.3274kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -11.896
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 24HA

Physicochemical properties
Molecular weight 323.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 1.11
Lipinski: ≤ 5
Rotatable bonds 4

Conformational strain (MMFF94s)
Strain energy (ΔE) 11.58kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 94.37kcal/mol
Minimised FF energy 82.78kcal/mol

SASA & burial

✓ computed
SASA (unbound) 540.9Ų
Total solvent-accessible surface area of free ligand
BSA total 532.1Ų
Buried surface area upon binding
BSA apolar 443.9Ų
Hydrophobic contacts buried
BSA polar 88.1Ų
Polar contacts buried
Fraction buried 98.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 83.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1581.0Ų
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 922.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)