FAIRMol

Z18704485

Pose ID 5287 Compound 2968 Pose 546

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 Z18704485
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
Weak or marginal quality
Binding strong Geometry medium Native strong SASA done
Strain ΔE
25.1 kcal/mol
Protein clashes
2
Internal clashes
3
Native overlap
contact recall 0.79, Jaccard 0.71, H-bond role recall 0.20
Burial
94%
Hydrophobic fit
80%
Reason: no major geometry red flags detected
2 protein-contact clashes 3 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.872 kcal/mol/HA) ✓ Good fit quality (FQ -8.23) ✓ Good H-bonds (5 bonds) ✓ Deep burial (94% SASA buried) ✓ Lipophilic contacts well-matched (80%) ✗ High strain energy (25.1 kcal/mol) ✗ Geometry warnings ✗ Minor protein-contact clashes (2) ✗ Internal clashes (8)
Score
-24.412
kcal/mol
LE
-0.872
kcal/mol/HA
Fit Quality
-8.23
FQ (Leeson)
HAC
28
heavy atoms
MW
379
Da
LogP
3.88
cLogP
Strain ΔE
25.1 kcal/mol
SASA buried
94%
Lipo contact
80% BSA apolar/total
SASA unbound
632 Ų
Apolar buried
479 Ų

Interaction summary

HB 5 HY 24 PI 2 CLASH 3

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 rank0.224Score-24.412
Inter norm-1.150Intra norm0.278
Top1000noExcludedno
Contacts17H-bonds5
Artifact reasongeometry warning; 8 clashes; 2 protein contact clashes; 2 severe cofactor-context clashes; moderate strain Δ 25.1
Residues
ARG14 ASP161 CYS168 GLY205 LEU208 LEU209 LYS178 MET163 MET213 NAP301 PHE97 PRO210 SER95 TRP221 TYR174 VAL206 VAL211

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 overlap15Native recall0.79
Jaccard0.71RMSD-
HB strict2Strict recall0.33
HB same residue+role1HB role recall0.20
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
546 0.2238301789647691 -1.14955 -24.4121 5 17 15 0.79 0.20 - no Current
543 1.9070443282796026 -1.0078 -10.6451 7 15 0 0.00 0.00 - no Open
561 2.023700145990084 -1.07527 -21.5942 11 24 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 -24.412kcal/mol
Ligand efficiency (LE) -0.8719kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.231
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 28HA

Physicochemical properties
Molecular weight 379.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.88
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 25.15kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 78.89kcal/mol
Minimised FF energy 53.74kcal/mol

SASA & burial

✓ computed
SASA (unbound) 631.6Ų
Total solvent-accessible surface area of free ligand
BSA total 594.7Ų
Buried surface area upon binding
BSA apolar 478.8Ų
Hydrophobic contacts buried
BSA polar 115.9Ų
Polar contacts buried
Fraction buried 94.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 80.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1657.5Ų
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 908.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)