FAIRMol

Z19459210

Pose ID 7813 Compound 944 Pose 361

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
T12
T. brucei R5P T. brucei
Ligand Z19459210
PDB6FXS↗

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
26.4 kcal/mol
Protein clashes
6
Internal clashes
6
Native overlap
contact recall 0.94, Jaccard 0.88, H-bond role recall 0.70
Burial
65%
Hydrophobic fit
57%
Reason: 6 internal clashes
6 protein-contact clashes 6 intramolecular clashes 48% of hydrophobic surface appears solvent-exposed (10/21 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.786 kcal/mol/HA) ✓ Good fit quality (FQ -7.73) ✓ Strong H-bond network (13 bonds) ✓ Deep burial (65% SASA buried) ✗ High strain energy (26.4 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (11)
Score
-25.164
kcal/mol
LE
-0.786
kcal/mol/HA
Fit Quality
-7.73
FQ (Leeson)
HAC
32
heavy atoms
MW
458
Da
LogP
3.57
cLogP
Strain ΔE
26.4 kcal/mol
SASA buried
65%
Lipo contact
57% BSA apolar/total
SASA unbound
744 Ų
Apolar buried
277 Ų

Interaction summary

HB 13 HY 7 PI 4 CLASH 6 ⚠ Exposure 47%
⚠️Partial hydrophobic solvent exposure
48% of hydrophobic surface appears solvent-exposed (10/21 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 21 Buried (contacted) 11 Exposed 10 LogP 3.57 H-bonds 13
Exposed fragments: phenyl (6/6 atoms exposed)aliphatic chain/group (4 atoms exposed)
Final rank5.606Score-25.164
Inter norm-1.029Intra norm0.243
Top1000noExcludedno
Contacts16H-bonds13
Artifact reasongeometry warning; 11 clashes; 3 protein clashes; moderate strain Δ 26.4
Residues
ARG140 ARG144 ASN106 HIS105 HIS141 ARG116 ARG46 CYS72 GLY73 GLY75 GLY77 HIS14 ILE15 ILE76 SER74 TYR49

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

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 overlap15Native recall0.94
Jaccard0.88RMSD-
HB strict9Strict recall0.75
HB same residue+role7HB role recall0.70
HB same residue8HB residue recall0.80

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

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
353 0.2677846330097941 -1.07537 -27.8222 8 17 0 0.00 0.00 - no Open
385 1.072504017808142 -0.997956 -27.1257 7 18 0 0.00 0.00 - no Open
335 1.9579738510770275 -1.01092 -28.7026 6 22 0 0.00 0.00 - no Open
382 2.0108526982107993 -0.822339 -20.3127 6 13 0 0.00 0.00 - no Open
380 2.3895493898087743 -0.733724 -19.5103 13 14 0 0.00 0.00 - no Open
451 2.500575774493837 -0.801352 -19.5984 4 18 0 0.00 0.00 - no Open
365 2.585210403258686 -0.744596 -11.1465 9 20 0 0.00 0.00 - no Open
397 3.1112027661132537 -0.667648 -14.8384 8 10 0 0.00 0.00 - no Open
398 3.193158610637237 -0.881209 -19.5521 15 18 0 0.00 0.00 - no Open
436 3.954326897652338 -0.726205 -12.1702 7 19 0 0.00 0.00 - no Open
337 4.153204340630617 -0.904158 -19.2488 9 13 0 0.00 0.00 - no Open
346 5.166667667365341 -0.742034 -19.6346 11 13 5 0.31 0.30 - no Open
361 5.606440624303128 -1.02946 -25.164 13 16 15 0.94 0.70 - no Current

Molecular metrics

RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
✓ Metrics available

Scoring & efficiency
Docking score -25.164kcal/mol
Ligand efficiency (LE) -0.7864kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.733
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 32HA

Physicochemical properties
Molecular weight 458.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.57
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 26.35kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 101.81kcal/mol
Minimised FF energy 75.45kcal/mol

SASA & burial

✓ computed
SASA (unbound) 743.7Ų
Total solvent-accessible surface area of free ligand
BSA total 485.1Ų
Buried surface area upon binding
BSA apolar 277.4Ų
Hydrophobic contacts buried
BSA polar 207.7Ų
Polar contacts buried
Fraction buried 65.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 57.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2162.8Ų
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 779.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)