FAIRMol

KB_Leish_184

Pose ID 4189 Compound 2905 Pose 126

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
T07
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
Reject SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
14.9 kcal/mol
Protein clashes
12
Internal clashes
12
Native overlap
contact recall 0.63, Jaccard 0.52, H-bond role recall 0.60
Burial
98%
Hydrophobic fit
84%
Reason: 12 protein-contact clashes, 12 internal clashes
12 protein-contact clashes 12 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-1.356 kcal/mol/HA) ✓ Good fit quality (FQ -12.15) ✓ Good H-bonds (5 bonds) ✓ Deep burial (98% SASA buried) ✓ Lipophilic contacts well-matched (84%) ✗ Moderate strain (14.9 kcal/mol) ✗ Geometry warnings ✗ Severe protein-contact clashes (14) ✗ Many internal clashes (13)
Score
-32.537
kcal/mol
LE
-1.356
kcal/mol/HA
Fit Quality
-12.15
FQ (Leeson)
HAC
24
heavy atoms
MW
323
Da
LogP
1.11
cLogP
Final rank
2.3916
rank score
Inter norm
-1.313
normalised
Contacts
16
H-bonds 11
Strain ΔE
14.9 kcal/mol
SASA buried
98%
Lipo contact
84% BSA apolar/total
SASA unbound
561 Ų
Apolar buried
465 Ų

Interaction summary

HBD 3 HBA 2 HY 6 PI 3 CLASH 12

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 4.

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 overlap12Native recall0.63
Jaccard0.52RMSD-
HB strict3Strict recall0.50
HB same residue+role3HB role recall0.60
HB same residue3HB residue recall0.60

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
164 1.5626524427287396 -1.40194 -31.8585 9 17 15 0.79 0.60 - no Open
126 2.3916176710034507 -1.31279 -32.5369 11 16 12 0.63 0.60 - no Current
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 -32.537kcal/mol
Ligand efficiency (LE) -1.3557kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -12.150
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) 14.89kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 99.63kcal/mol
Minimised FF energy 84.74kcal/mol

SASA & burial

✓ computed
SASA (unbound) 561.4Ų
Total solvent-accessible surface area of free ligand
BSA total 551.9Ų
Buried surface area upon binding
BSA apolar 465.4Ų
Hydrophobic contacts buried
BSA polar 86.5Ų
Polar contacts buried
Fraction buried 98.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 84.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1602.5Ų
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 922.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)