FAIRMol

Z56842318

Pose ID 4636 Compound 2769 Pose 573

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
T07
T. brucei PTR1 T. brucei
Ligand Z56842318
PDB6RX6↗

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
34.7 kcal/mol
Protein clashes
0
Internal clashes
17
Native overlap
contact recall 0.74, Jaccard 0.67, H-bond role recall 0.20
Burial
95%
Hydrophobic fit
89%
Reason: 17 internal clashes
17 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.925 kcal/mol/HA) ✓ Good fit quality (FQ -8.53) ✓ Deep burial (95% SASA buried) ✓ Lipophilic contacts well-matched (89%) ✗ Very high strain energy (34.7 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (17)
Score
-24.061
kcal/mol
LE
-0.925
kcal/mol/HA
Fit Quality
-8.53
FQ (Leeson)
HAC
26
heavy atoms
MW
362
Da
LogP
5.19
cLogP
Strain ΔE
34.7 kcal/mol
SASA buried
95%
Lipo contact
89% BSA apolar/total
SASA unbound
581 Ų
Apolar buried
492 Ų

Interaction summary

HB 1 HY 24 PI 5 CLASH 0

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
No clash · clashes detected for this pose.
Final rank0.658Score-24.061
Inter norm-1.191Intra norm0.265
Top1000noExcludedno
Contacts16H-bonds1
Artifact reasongeometry warning; 17 clashes; 1 severe cofactor-context clash; high strain Δ 34.7
Residues
ARG14 CYS168 GLY205 LEU208 LEU209 LEU263 MET163 MET213 NAP301 PHE97 PRO210 SER207 SER95 TRP221 TYR174 VAL206

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
Jaccard0.67RMSD-
HB strict0Strict recall0.00
HB same residue+role1HB role recall0.20
HB same residue1HB residue recall0.20

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
573 0.658367749183348 -1.19081 -24.0608 1 16 14 0.74 0.20 - no Current
586 2.2558334122238293 -1.3034 -31.1692 4 20 0 0.00 0.00 - no Open
617 2.7230584134012368 -0.908652 -20.3799 4 17 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 -24.061kcal/mol
Ligand efficiency (LE) -0.9254kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.526
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 26HA

Physicochemical properties
Molecular weight 361.8Da
Lipinski: ≤ 500 Da
LogP (cLogP) 5.19
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 34.70kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 59.48kcal/mol
Minimised FF energy 24.77kcal/mol

SASA & burial

✓ computed
SASA (unbound) 581.2Ų
Total solvent-accessible surface area of free ligand
BSA total 551.5Ų
Buried surface area upon binding
BSA apolar 492.3Ų
Hydrophobic contacts buried
BSA polar 59.2Ų
Polar contacts buried
Fraction buried 94.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 89.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1667.0Ų
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 906.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)