FAIRMol

KB_Leish_92

Pose ID 7550 Compound 308 Pose 98

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
T12
T. brucei R5P T. brucei
Ligand KB_Leish_92
PDB6FXS↗

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
66.3 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 1.00, Jaccard 1.00, H-bond role recall 0.30
Burial
72%
Hydrophobic fit
78%
Reason: strain 66.3 kcal/mol
strain ΔE 66.3 kcal/mol 5 protein-contact clashes 5 intramolecular clashes 55% of hydrophobic surface appears solvent-exposed (11/20 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-1.020 kcal/mol/HA) ✓ Good fit quality (FQ -9.51) ✓ Strong H-bond network (10 bonds) ✓ Deep burial (72% SASA buried) ✓ Lipophilic contacts well-matched (78%) ✗ Extreme strain energy (66.3 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (10)
Score
-27.531
kcal/mol
LE
-1.020
kcal/mol/HA
Fit Quality
-9.51
FQ (Leeson)
HAC
27
heavy atoms
MW
359
Da
LogP
2.13
cLogP
Strain ΔE
66.3 kcal/mol
SASA buried
72%
Lipo contact
78% BSA apolar/total
SASA unbound
641 Ų
Apolar buried
360 Ų

Interaction summary

HB 10 HY 11 PI 2 CLASH 5 ⚠ Exposure 55%

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
⚠️Partial hydrophobic solvent exposure
55% of hydrophobic surface appears solvent-exposed (11/20 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 20 Buried (contacted) 9 Exposed 11 LogP 2.13 H-bonds 10
Exposed fragments: phenyl (5/6 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (2 atoms exposed)
Final rank3.940Score-27.531
Inter norm-0.990Intra norm-0.029
Top1000noExcludedno
Contacts16H-bonds10
Artifact reasongeometry warning; 10 clashes; 2 protein clashes; high strain Δ 66.3
Residues
ARG140 ARG144 ASN106 HIS105 HIS141 ARG46 ASP13 CYS72 GLY73 GLY75 GLY77 HIS14 ILE15 ILE76 SER74 TYR49

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name6FXSContacts16
PoseOpen native poseHB0
IFP residues
ARG140 ARG144 ASN106 HIS105 HIS141 ARG46 ASP13 CYS72 GLY73 GLY75 GLY77 HIS14 ILE15 ILE76 SER74 TYR49
Current overlap16Native recall1.00
Jaccard1.00RMSD-
HB strict5Strict recall0.42
HB same residue+role3HB role recall0.30
HB same residue4HB residue recall0.40

Protein summary

302 residues
Protein targetT12Atoms4598
Residues302Chains2
Residue summaryARG:576; ILE:456; VAL:448; GLU:360; ALA:340; LEU:304; TYR:252; HIS:204; PRO:196; THR:196; GLY:182; LYS:176; ASP:168; PHE:160; MET:153; SER:121

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:CSD72

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
472 0.4377893302794625 -0.950392 -26.2449 0 11 0 0.00 0.00 - no Open
70 0.47106599804211174 -0.932342 -26.3572 0 12 0 0.00 0.00 - no Open
468 0.6892648734294643 -1.20281 -32.8902 7 13 0 0.00 0.00 - no Open
435 1.2154656197774207 -1.20918 -33.9917 9 16 0 0.00 0.00 - no Open
509 1.673956140477069 -1.03134 -29.6551 2 15 0 0.00 0.00 - no Open
519 1.9262872169038363 -0.995405 -29.7653 2 14 0 0.00 0.00 - no Open
494 3.039605889023859 -1.13239 -31.7742 5 15 0 0.00 0.00 - no Open
454 3.2164434138782974 -1.00198 -27.9483 10 16 16 1.00 0.40 - no Open
478 3.3020607865760265 -0.914987 -27.3309 9 15 1 0.06 0.00 - no Open
479 3.505705638707487 -0.714533 -21.8412 6 11 0 0.00 0.00 - no Open
496 3.6376046883594673 -0.802309 -23.1254 6 12 0 0.00 0.00 - no Open
98 3.939670025094264 -0.990476 -27.5314 10 16 16 1.00 0.30 - no Current
160 4.374456075611729 -0.732508 -20.3753 8 11 0 0.00 0.00 - no Open
117 4.576376594729494 -1.06666 -30.2454 6 15 0 0.00 0.00 - no Open
455 6.222747976212252 -1.01947 -28.54 12 16 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 -27.531kcal/mol
Ligand efficiency (LE) -1.0197kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.513
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 27HA

Physicochemical properties
Molecular weight 359.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.13
Lipinski: ≤ 5
Rotatable bonds 3

Conformational strain (MMFF94s)
Strain energy (ΔE) 66.32kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 175.06kcal/mol
Minimised FF energy 108.74kcal/mol

SASA & burial

✓ computed
SASA (unbound) 641.5Ų
Total solvent-accessible surface area of free ligand
BSA total 464.5Ų
Buried surface area upon binding
BSA apolar 360.4Ų
Hydrophobic contacts buried
BSA polar 104.1Ų
Polar contacts buried
Fraction buried 72.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 77.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2196.7Ų
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 2454.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 795.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)