FAIRMol

Z25403962

Pose ID 5249 Compound 2960 Pose 508

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 Z25403962
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
14.6 kcal/mol
Protein clashes
2
Internal clashes
5
Native overlap
contact recall 0.63, Jaccard 0.52, H-bond role recall 0.20
Burial
94%
Hydrophobic fit
69%
Reason: no major geometry red flags detected
2 protein-contact clashes 5 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.604 kcal/mol/HA) ✓ Good fit quality (FQ -13.93) ✓ Good H-bonds (5 bonds) ✓ Deep burial (94% SASA buried) ✓ Lipophilic contacts well-matched (69%) ✗ Moderate strain (14.6 kcal/mol) ✗ Geometry warnings ✗ Minor protein-contact clashes (3) ✗ Many internal clashes (10)
Score
-35.296
kcal/mol
LE
-1.604
kcal/mol/HA
Fit Quality
-13.93
FQ (Leeson)
HAC
22
heavy atoms
MW
324
Da
LogP
4.45
cLogP
Strain ΔE
14.6 kcal/mol
SASA buried
94%
Lipo contact
69% BSA apolar/total
SASA unbound
564 Ų
Apolar buried
366 Ų

Interaction summary

HB 5 HY 24 PI 3 CLASH 5

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 rank0.087Score-35.296
Inter norm-1.456Intra norm-0.148
Top1000noExcludedno
Contacts16H-bonds5
Artifact reasongeometry warning; 10 clashes; 3 protein contact clashes; 1 severe cofactor-context clash
Residues
ARG14 ASP161 CYS168 GLY205 LEU208 LEU209 LEU263 LYS224 MET163 NAP301 PHE97 PRO210 TRP221 TYR174 VAL206 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
Jaccard0.52RMSD-
HB strict1Strict recall0.17
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
508 0.08703222788999707 -1.45603 -35.2964 5 16 12 0.63 0.20 - no Current
502 1.4794874206897541 -1.33391 -33.7698 13 15 0 0.00 0.00 - no Open
505 4.274286380505308 -1.09506 -28.318 13 18 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 -35.296kcal/mol
Ligand efficiency (LE) -1.6044kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -13.929
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 22HA

Physicochemical properties
Molecular weight 324.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.45
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 14.62kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 29.02kcal/mol
Minimised FF energy 14.40kcal/mol

SASA & burial

✓ computed
SASA (unbound) 563.5Ų
Total solvent-accessible surface area of free ligand
BSA total 531.5Ų
Buried surface area upon binding
BSA apolar 365.5Ų
Hydrophobic contacts buried
BSA polar 166.0Ų
Polar contacts buried
Fraction buried 94.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 68.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1519.6Ų
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 929.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)