FAIRMol

Z55294982

Pose ID 5364 Compound 2946 Pose 623

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
T08
T. brucei PTR1 T. brucei
Ligand Z55294982
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
27.3 kcal/mol
Protein clashes
0
Internal clashes
9
Native overlap
contact recall 0.63, Jaccard 0.57, H-bond role recall 0.40
Burial
85%
Hydrophobic fit
86%
Reason: 9 internal clashes
9 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.131 kcal/mol/HA) ✓ Good fit quality (FQ -10.55) ✓ Good H-bonds (3 bonds) ✓ Deep burial (85% SASA buried) ✓ Lipophilic contacts well-matched (86%) ✗ High strain energy (27.3 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (9)
Score
-30.538
kcal/mol
LE
-1.131
kcal/mol/HA
Fit Quality
-10.55
FQ (Leeson)
HAC
27
heavy atoms
MW
428
Da
LogP
4.81
cLogP
Final rank
-0.2364
rank score
Inter norm
-1.247
normalised
Contacts
14
H-bonds 8
Strain ΔE
27.3 kcal/mol
SASA buried
85%
Lipo contact
86% BSA apolar/total
SASA unbound
653 Ų
Apolar buried
479 Ų

Interaction summary

HBD 3 HY 6 PI 1 CLASH 0

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 1.

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.

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: permissive.
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
Jaccard0.57RMSD-
HB strict3Strict recall0.50
HB same residue+role2HB role recall0.40
HB same residue2HB residue recall0.40

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
623 -0.23635818283349871 -1.24653 -30.538 8 14 12 0.63 0.40 - no Current
656 3.7896172684657228 -1.13262 -31.6822 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 -30.538kcal/mol
Ligand efficiency (LE) -1.1310kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.552
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 27HA

Physicochemical properties
Molecular weight 428.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.81
Lipinski: ≤ 5
Rotatable bonds 4

Conformational strain (MMFF94s)
Strain energy (ΔE) 27.27kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -55.49kcal/mol
Minimised FF energy -82.76kcal/mol

SASA & burial

✓ computed
SASA (unbound) 652.8Ų
Total solvent-accessible surface area of free ligand
BSA total 557.1Ų
Buried surface area upon binding
BSA apolar 478.5Ų
Hydrophobic contacts buried
BSA polar 78.5Ų
Polar contacts buried
Fraction buried 85.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 85.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1664.5Ų
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 952.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)