FAIRMol

Z56891526

Pose ID 4578 Compound 1977 Pose 515

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 Z56891526
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
36.9 kcal/mol
Protein clashes
1
Internal clashes
2
Native overlap
contact recall 0.74, Jaccard 0.74, H-bond role recall 0.60
Burial
96%
Hydrophobic fit
69%
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.833 kcal/mol/HA) ✓ Good fit quality (FQ -15.02) ✓ Strong H-bond network (13 bonds) ✓ Deep burial (96% SASA buried) ✓ Lipophilic contacts well-matched (69%) ✗ Very high strain energy (36.9 kcal/mol) ✗ Geometry warnings ✗ Minor protein-contact clashes (2) ✗ Internal clashes (5)
Score
-34.823
kcal/mol
LE
-1.833
kcal/mol/HA
Fit Quality
-15.02
FQ (Leeson)
HAC
19
heavy atoms
MW
279
Da
LogP
1.39
cLogP
Strain ΔE
36.9 kcal/mol
SASA buried
96%
Lipo contact
69% BSA apolar/total
SASA unbound
483 Ų
Apolar buried
318 Ų

Interaction summary

HB 13 HY 18 PI 3 CLASH 2

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 rank-0.893Score-34.823
Inter norm-1.945Intra norm0.112
Top1000noExcludedno
Contacts14H-bonds13
Artifact reasongeometry warning; 5 clashes; 2 protein contact clashes; 1 severe cofactor-context clash; high strain Δ 36.9
Residues
ARG14 ASP161 CYS168 GLY205 LEU209 MET213 NAP301 PHE171 PHE97 SER207 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 overlap14Native recall0.74
Jaccard0.74RMSD-
HB strict4Strict recall0.67
HB same residue+role3HB role recall0.60
HB same residue3HB residue recall0.60

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
515 -0.8932265087012629 -1.94463 -34.8227 13 14 14 0.74 0.60 - no Current
527 0.6368868812026727 -1.76246 -30.9977 11 14 14 0.74 0.60 - no Open
518 0.7189251085272259 -1.53696 -22.1625 8 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 -34.823kcal/mol
Ligand efficiency (LE) -1.8328kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -15.023
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 19HA

Physicochemical properties
Molecular weight 279.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) 1.39
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 36.91kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 94.20kcal/mol
Minimised FF energy 57.29kcal/mol

SASA & burial

✓ computed
SASA (unbound) 482.8Ų
Total solvent-accessible surface area of free ligand
BSA total 461.1Ų
Buried surface area upon binding
BSA apolar 318.4Ų
Hydrophobic contacts buried
BSA polar 142.7Ų
Polar contacts buried
Fraction buried 95.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 69.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1468.8Ų
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 913.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)