FAIRMol

Z28419783

Pose ID 5135 Compound 392 Pose 394

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
T08
T. brucei PTR1 T. brucei
Ligand Z28419783
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
60.8 kcal/mol
Protein clashes
2
Internal clashes
4
Native overlap
contact recall 0.63, Jaccard 0.44, H-bond role recall 0.40
Burial
90%
Hydrophobic fit
80%
Reason: strain 60.8 kcal/mol
strain ΔE 60.8 kcal/mol 2 protein-contact clashes 4 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.976 kcal/mol/HA) ✓ Good fit quality (FQ -9.76) ✓ Strong H-bond network (6 bonds) ✓ Deep burial (90% SASA buried) ✓ Lipophilic contacts well-matched (80%) ✗ Extreme strain energy (60.8 kcal/mol) ✗ Geometry warnings ✗ Minor protein-contact clashes (2) ✗ Internal clashes (9)
Score
-33.179
kcal/mol
LE
-0.976
kcal/mol/HA
Fit Quality
-9.76
FQ (Leeson)
HAC
34
heavy atoms
MW
478
Da
LogP
5.08
cLogP
Strain ΔE
60.8 kcal/mol
SASA buried
90%
Lipo contact
80% BSA apolar/total
SASA unbound
754 Ų
Apolar buried
543 Ų

Interaction summary

HB 6 HY 24 PI 5 CLASH 4

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 rank0.519Score-33.179
Inter norm-0.973Intra norm-0.003
Top1000noExcludedno
Contacts20H-bonds6
Artifact reasongeometry warning; 9 clashes; 2 protein contact clashes; 3 cofactor-context clashes; high strain Δ 60.8
Residues
ARG14 ASN175 ASP161 CYS168 GLN166 GLY205 LEU263 MET163 NAP301 PHE171 PHE97 PRO167 PRO210 SER95 TRP221 TYR174 VAL164 VAL206 VAL211 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 overlap12Native recall0.63
Jaccard0.44RMSD-
HB strict1Strict recall0.17
HB same residue+role2HB role recall0.40
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
394 0.5194059874261302 -0.973113 -33.1789 6 20 12 0.63 0.40 - no Current
470 2.3012483912121358 -0.835739 -30.149 4 18 0 0.00 0.00 - no Open
376 2.5541271605381515 -0.748382 -25.4446 5 13 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 -33.179kcal/mol
Ligand efficiency (LE) -0.9758kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.764
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 34HA

Physicochemical properties
Molecular weight 477.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 5.08
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 60.80kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 81.82kcal/mol
Minimised FF energy 21.02kcal/mol

SASA & burial

✓ computed
SASA (unbound) 754.4Ų
Total solvent-accessible surface area of free ligand
BSA total 677.8Ų
Buried surface area upon binding
BSA apolar 543.3Ų
Hydrophobic contacts buried
BSA polar 134.5Ų
Polar contacts buried
Fraction buried 89.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 80.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1713.8Ų
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 2051.9Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 931.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)