FAIRMol

Z68196981

Pose ID 5118 Compound 3137 Pose 377

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 Z68196981
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
40.4 kcal/mol
Protein clashes
4
Internal clashes
11
Native overlap
contact recall 0.74, Jaccard 0.70, H-bond role recall 0.20
Burial
96%
Hydrophobic fit
84%
Reason: 11 internal clashes
4 protein-contact clashes 11 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-1.058 kcal/mol/HA) ✓ Good fit quality (FQ -9.87) ✓ Good H-bonds (4 bonds) ✓ Deep burial (96% SASA buried) ✓ Lipophilic contacts well-matched (84%) ✗ Extreme strain energy (40.4 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (7)
Score
-28.563
kcal/mol
LE
-1.058
kcal/mol/HA
Fit Quality
-9.87
FQ (Leeson)
HAC
27
heavy atoms
MW
409
Da
LogP
3.86
cLogP
Strain ΔE
40.4 kcal/mol
SASA buried
96%
Lipo contact
84% BSA apolar/total
SASA unbound
604 Ų
Apolar buried
486 Ų

Interaction summary

HB 4 HY 24 PI 3 CLASH 11
Final rank2.552Score-28.563
Inter norm-1.244Intra norm0.186
Top1000noExcludedno
Contacts15H-bonds4
Artifact reasongeometry warning; 7 clashes; 2 protein clashes; 8 cofactor-context clashes; high strain Δ 40.4
Residues
ARG14 ASP161 CYS168 GLY205 LEU208 LEU209 MET163 MET213 NAP301 PHE97 PRO210 SER207 TRP221 TYR174 VAL206

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

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 overlap14Native recall0.74
Jaccard0.70RMSD-
HB strict1Strict recall0.17
HB same residue+role1HB role recall0.20
HB same residue3HB residue recall0.60

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
322 2.3925272315952335 -1.15762 -28.8691 8 21 0 0.00 0.00 - no Open
377 2.5521677916786434 -1.24386 -28.5631 4 15 14 0.74 0.20 - no Current
427 4.7556666878739176 -0.889974 -20.5227 9 19 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 -28.563kcal/mol
Ligand efficiency (LE) -1.0579kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.870
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 27HA

Physicochemical properties
Molecular weight 408.9Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.86
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 40.45kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -5.67kcal/mol
Minimised FF energy -46.12kcal/mol

SASA & burial

✓ computed
SASA (unbound) 604.3Ų
Total solvent-accessible surface area of free ligand
BSA total 579.8Ų
Buried surface area upon binding
BSA apolar 486.4Ų
Hydrophobic contacts buried
BSA polar 93.4Ų
Polar contacts buried
Fraction buried 95.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 83.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1639.7Ų
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 2051.9Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 917.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)