FAIRMol

Z54323248

Pose ID 5343 Compound 1671 Pose 602

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 Z54323248
PDB6RX6↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
61.9 kcal/mol
Protein clashes
4
Internal clashes
10
Native overlap
contact recall 0.63, Jaccard 0.55, H-bond role recall 0.80
Burial
93%
Hydrophobic fit
61%
Reason: 10 internal clashes, strain 61.9 kcal/mol
strain ΔE 61.9 kcal/mol 4 protein-contact clashes 10 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.985 kcal/mol/HA) ✓ Good fit quality (FQ -9.29) ✓ Strong H-bond network (14 bonds) ✓ Deep burial (93% SASA buried) ✓ Lipophilic contacts well-matched (61%) ✗ Extreme strain energy (61.9 kcal/mol) ✗ Geometry warnings ✗ Minor protein-contact clashes (4) ✗ Many internal clashes (10)
Score
-27.570
kcal/mol
LE
-0.985
kcal/mol/HA
Fit Quality
-9.29
FQ (Leeson)
HAC
28
heavy atoms
MW
421
Da
LogP
2.71
cLogP
Strain ΔE
61.9 kcal/mol
SASA buried
93%
Lipo contact
61% BSA apolar/total
SASA unbound
655 Ų
Apolar buried
371 Ų

Interaction summary

HB 14 HY 21 PI 2 CLASH 0
Final rank0.778Score-27.570
Inter norm-1.135Intra norm0.129
Top1000noExcludedno
Contacts15H-bonds14
Artifact reasongeometry warning; 10 clashes; 4 protein contact clashes; 2 cofactor-context clashes; high strain Δ 61.9
Residues
ARG14 ASP161 CYS168 GLY205 LEU208 LEU209 LYS13 MET163 NAP301 PHE97 PRO210 TRP221 TYR174 VAL206 VAL211

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

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
Jaccard0.55RMSD-
HB strict5Strict recall0.83
HB same residue+role4HB role recall0.80
HB same residue4HB residue recall0.80

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.

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
619 0.48041461483005266 -0.858102 -22.0509 5 12 0 0.00 0.00 - no Open
602 0.7782551913172737 -1.13541 -27.5699 14 15 12 0.63 0.80 - no Current
639 3.2764256629868695 -1.08077 -27.3404 8 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 -27.570kcal/mol
Ligand efficiency (LE) -0.9846kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.295
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 28HA

Physicochemical properties
Molecular weight 421.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.71
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 61.94kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 96.86kcal/mol
Minimised FF energy 34.92kcal/mol

SASA & burial

✓ computed
SASA (unbound) 655.4Ų
Total solvent-accessible surface area of free ligand
BSA total 611.4Ų
Buried surface area upon binding
BSA apolar 370.7Ų
Hydrophobic contacts buried
BSA polar 240.7Ų
Polar contacts buried
Fraction buried 93.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 60.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1516.5Ų
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 934.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)