FAIRMol

Z19456272

Pose ID 7899 Compound 100 Pose 447

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
T12
T. brucei R5P T. brucei
Ligand Z19456272
PDB6FXS↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
20.2 kcal/mol
Protein clashes
6
Internal clashes
6
Native overlap
contact recall 0.94, Jaccard 0.88, H-bond role recall 0.50
Burial
73%
Hydrophobic fit
68%
Reason: 6 internal clashes
6 protein-contact clashes 6 intramolecular clashes 35% of hydrophobic surface appears solvent-exposed (7/20 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.727 kcal/mol/HA) ✓ Good fit quality (FQ -7.08) ✓ Strong H-bond network (9 bonds) ✓ Deep burial (73% SASA buried) ✓ Lipophilic contacts well-matched (68%) ✗ High strain energy (20.2 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (8)
Score
-22.536
kcal/mol
LE
-0.727
kcal/mol/HA
Fit Quality
-7.08
FQ (Leeson)
HAC
31
heavy atoms
MW
462
Da
LogP
2.78
cLogP
Strain ΔE
20.2 kcal/mol
SASA buried
73%
Lipo contact
68% BSA apolar/total
SASA unbound
705 Ų
Apolar buried
347 Ų

Interaction summary

HB 9 HY 10 PI 5 CLASH 6 ⚠ Exposure 35%

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
⚠️Partial hydrophobic solvent exposure
35% of hydrophobic surface appears solvent-exposed (7/20 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 20 Buried (contacted) 13 Exposed 7 LogP 2.78 H-bonds 9
Exposed fragments: phenyl (6/6 atoms exposed)phenyl (3/5 atoms exposed)
Final rank2.859Score-22.536
Inter norm-0.882Intra norm0.155
Top1000noExcludedno
Contacts16H-bonds9
Artifact reasongeometry warning; 8 clashes; 1 protein clash; moderate strain Δ 20.2
Residues
ARG140 ARG144 ASN106 HIS105 HIS141 MET101 ARG46 ASP13 CYS72 GLY73 GLY77 HIS14 ILE15 ILE76 SER74 TYR49

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name6FXSContacts16
PoseOpen native poseHB0
IFP residues
ARG140 ARG144 ASN106 HIS105 HIS141 ARG46 ASP13 CYS72 GLY73 GLY75 GLY77 HIS14 ILE15 ILE76 SER74 TYR49
Current overlap15Native recall0.94
Jaccard0.88RMSD-
HB strict6Strict recall0.50
HB same residue+role5HB role recall0.50
HB same residue6HB residue recall0.60

Protein summary

302 residues
Protein targetT12Atoms4598
Residues302Chains2
Residue summaryARG:576; ILE:456; VAL:448; GLU:360; ALA:340; LEU:304; TYR:252; HIS:204; PRO:196; THR:196; GLY:182; LYS:176; ASP:168; PHE:160; MET:153; SER:121

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:CSD72

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
458 0.27097943228209714 -0.811185 -19.6635 2 14 0 0.00 0.00 - no Open
513 0.9544730494110983 -0.848599 -22.718 5 16 0 0.00 0.00 - no Open
139 1.2196504051403532 -0.732121 -21.3242 5 16 0 0.00 0.00 - no Open
506 1.3741049807450607 -0.848148 -20.44 3 19 0 0.00 0.00 - no Open
114 1.8007768117229013 -0.767307 -20.1444 8 15 0 0.00 0.00 - no Open
131 1.8058017168282356 -0.940039 -24.6674 6 14 0 0.00 0.00 - no Open
117 2.0182178879377184 -0.829303 -24.0955 5 14 0 0.00 0.00 - no Open
485 2.0994881049338083 -0.856427 -22.7639 4 13 0 0.00 0.00 - no Open
105 2.2832214801183897 -0.874039 -22.0808 4 17 0 0.00 0.00 - no Open
453 2.83121549954444 -0.908661 -22.7336 12 15 5 0.31 0.20 - no Open
447 2.8591163001678837 -0.882026 -22.5359 9 16 15 0.94 0.50 - no Current
525 2.939096492500812 -0.773608 -21.4384 5 12 0 0.00 0.00 - no Open
64 2.9866007130431282 -0.949521 -25.285 13 16 5 0.31 0.20 - no Open
450 3.435617077931159 -1.00835 -28.0542 9 19 0 0.00 0.00 - no Open
91 3.5725886357035477 -0.950541 -26.1853 11 15 5 0.31 0.20 - no Open
89 3.588860201862459 -0.897555 -24.8412 10 10 8 0.50 0.30 - no Open
425 4.484716716621432 -0.989791 -28.8598 6 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 -22.536kcal/mol
Ligand efficiency (LE) -0.7270kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.082
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 31HA

Physicochemical properties
Molecular weight 461.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.78
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 20.24kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 26.89kcal/mol
Minimised FF energy 6.66kcal/mol

SASA & burial

✓ computed
SASA (unbound) 705.4Ų
Total solvent-accessible surface area of free ligand
BSA total 512.5Ų
Buried surface area upon binding
BSA apolar 346.6Ų
Hydrophobic contacts buried
BSA polar 165.9Ų
Polar contacts buried
Fraction buried 72.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 67.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2163.1Ų
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 2454.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 771.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)