FAIRMol

Z234853480

Pose ID 4514 Compound 2652 Pose 451

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
T07
T. brucei PTR1 T. brucei
Ligand Z234853480
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 medium Native mixed SASA done
Strain ΔE
12.2 kcal/mol
Protein clashes
0
Internal clashes
3
Native overlap
contact recall 0.53, Jaccard 0.50, H-bond role recall 0.40
Burial
98%
Hydrophobic fit
71%
Reason: no major geometry red flags detected
3 intramolecular clashes
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.783 kcal/mol/HA) ✓ Good fit quality (FQ -13.57) ✓ Strong H-bond network (6 bonds) ✓ Deep burial (98% SASA buried) ✓ Lipophilic contacts well-matched (71%) ✗ Moderate strain (12.2 kcal/mol) ✗ Geometry warnings
Score
-28.532
kcal/mol
LE
-1.783
kcal/mol/HA
Fit Quality
-13.57
FQ (Leeson)
HAC
16
heavy atoms
MW
234
Da
LogP
2.07
cLogP
Strain ΔE
12.2 kcal/mol
SASA buried
98%
Lipo contact
71% BSA apolar/total
SASA unbound
427 Ų
Apolar buried
295 Ų

Interaction summary

HB 6 HY 16 PI 3 CLASH 0

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.
Final rank-1.508Score-28.532
Inter norm-1.898Intra norm0.115
Top1000noExcludedno
Contacts11H-bonds6
Artifact reasongeometry warning; 3 clashes; 2 severe cofactor-context clashes
Residues
ARG14 CYS168 GLY205 LEU209 LEU263 NAP301 PHE97 SER95 TRP221 TYR174 VAL206

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 overlap10Native recall0.53
Jaccard0.50RMSD-
HB strict3Strict recall0.50
HB same residue+role2HB role recall0.40
HB same residue2HB residue recall0.40

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

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
451 -1.5078063148624512 -1.89844 -28.5321 6 11 10 0.53 0.40 - no Current
482 0.9816984890533861 -1.65262 -24.0361 8 15 0 0.00 0.00 - no Open
482 1.1445978680261857 -1.41808 -21.6735 6 9 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 -28.532kcal/mol
Ligand efficiency (LE) -1.7833kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -13.574
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 16HA

Physicochemical properties
Molecular weight 234.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.07
Lipinski: ≤ 5
Rotatable bonds 3

Conformational strain (MMFF94s)
Strain energy (ΔE) 12.23kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 29.54kcal/mol
Minimised FF energy 17.31kcal/mol

SASA & burial

✓ computed
SASA (unbound) 426.6Ų
Total solvent-accessible surface area of free ligand
BSA total 418.7Ų
Buried surface area upon binding
BSA apolar 295.4Ų
Hydrophobic contacts buried
BSA polar 123.3Ų
Polar contacts buried
Fraction buried 98.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 70.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1428.4Ų
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 921.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)