FAIRMol

Z57108748

Pose ID 4448 Compound 2676 Pose 385

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
T07
T. brucei PTR1 T. brucei
Ligand Z57108748
PDB6RX6↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Promising SASA cached
Promising and worth follow-up
Binding strong Geometry high Native strong SASA done
Strain ΔE
13.9 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.63, Jaccard 0.63, H-bond role recall 0.40
Burial
97%
Hydrophobic fit
75%
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.595 kcal/mol/HA) ✓ Good fit quality (FQ -13.07) ✓ Strong H-bond network (8 bonds) ✓ Deep burial (97% SASA buried) ✓ Lipophilic contacts well-matched (75%) ✗ Moderate strain (13.9 kcal/mol) ✗ Geometry warnings ✗ Minor protein-contact clashes (2) ✗ Internal clashes (9)
Score
-30.297
kcal/mol
LE
-1.595
kcal/mol/HA
Fit Quality
-13.07
FQ (Leeson)
HAC
19
heavy atoms
MW
254
Da
LogP
2.87
cLogP
Strain ΔE
13.9 kcal/mol
SASA buried
97%
Lipo contact
75% BSA apolar/total
SASA unbound
455 Ų
Apolar buried
331 Ų

Interaction summary

HB 8 HY 22 PI 2 CLASH 1
Final rank-0.231Score-30.297
Inter norm-1.721Intra norm0.126
Top1000noExcludedno
Contacts12H-bonds8
Artifact reasongeometry warning; 9 clashes; 2 protein contact clashes; 1 severe cofactor-context clash
Residues
ARG14 CYS168 GLY205 LEU208 LEU209 NAP301 PHE97 PRO210 SER207 TRP221 TYR174 VAL206

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

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
Jaccard0.63RMSD-
HB strict3Strict recall0.50
HB same residue+role2HB role recall0.40
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
385 -0.23094152859741754 -1.72071 -30.2969 8 12 12 0.63 0.40 - no Current
395 2.6689546735600196 -1.42954 -24.9999 6 16 0 0.00 0.00 - no Open
417 2.870564801938861 -1.33148 -21.9216 5 13 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 -30.297kcal/mol
Ligand efficiency (LE) -1.5946kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -13.070
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 19HA

Physicochemical properties
Molecular weight 254.2Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.87
Lipinski: ≤ 5
Rotatable bonds 3

Conformational strain (MMFF94s)
Strain energy (ΔE) 13.85kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 70.19kcal/mol
Minimised FF energy 56.34kcal/mol

SASA & burial

✓ computed
SASA (unbound) 455.4Ų
Total solvent-accessible surface area of free ligand
BSA total 443.2Ų
Buried surface area upon binding
BSA apolar 330.7Ų
Hydrophobic contacts buried
BSA polar 112.6Ų
Polar contacts buried
Fraction buried 97.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 74.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1471.6Ų
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 922.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)