FAIRMol

Z275025498

Pose ID 7807 Compound 760 Pose 355

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 Z275025498
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
Weak or marginal quality
Binding strong Geometry high Native strong SASA done
Strain ΔE
23.1 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 1.00, Jaccard 0.80, H-bond role recall 0.40
Burial
74%
Hydrophobic fit
52%
Reason: no major geometry red flags detected
2 protein-contact clashes 41% of hydrophobic surface appears solvent-exposed (7/17 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 (-1.081 kcal/mol/HA) ✓ Good fit quality (FQ -10.21) ✓ Strong H-bond network (11 bonds) ✓ Deep burial (74% SASA buried) ✗ High strain energy (23.1 kcal/mol) ✗ Geometry warnings ✗ Protein-contact clashes (9) ✗ Internal clashes (7)
Score
-30.273
kcal/mol
LE
-1.081
kcal/mol/HA
Fit Quality
-10.21
FQ (Leeson)
HAC
28
heavy atoms
MW
430
Da
LogP
3.57
cLogP
Strain ΔE
23.1 kcal/mol
SASA buried
74%
Lipo contact
52% BSA apolar/total
SASA unbound
628 Ų
Apolar buried
241 Ų

Interaction summary

HB 11 HY 7 PI 4 CLASH 2 ⚠ Exposure 41%

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
41% of hydrophobic surface appears solvent-exposed (7/17 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 17 Buried (contacted) 10 Exposed 7 LogP 3.57 H-bonds 11
Exposed fragments: phenyl (6/6 atoms exposed)aliphatic chain/group (1 atom exposed)
Final rank1.306Score-30.273
Inter norm-1.048Intra norm-0.033
Top1000noExcludedno
Contacts20H-bonds11
Artifact reasongeometry warning; 7 clashes; 9 protein contact clashes; moderate strain Δ 21.7
Residues
ARG140 ARG144 ASN106 HIS105 HIS141 MET101 TYR97 ARG116 ARG46 ASP13 CYS72 GLY73 GLY75 GLY77 HIS14 ILE15 ILE76 MET78 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 overlap16Native recall1.00
Jaccard0.80RMSD-
HB strict4Strict recall0.33
HB same residue+role4HB role recall0.40
HB same residue5HB residue recall0.50

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
381 0.4678678754036258 -1.1526 -33.9568 4 15 0 0.00 0.00 - no Open
360 0.5197055751298865 -0.90829 -27.5829 3 17 0 0.00 0.00 - no Open
447 1.219696433124539 -0.981399 -29.5048 3 18 0 0.00 0.00 - no Open
355 1.3063524923317955 -1.04791 -30.2735 11 20 16 1.00 0.40 - no Current
408 1.743798155616244 -1.05333 -31.9361 3 16 0 0.00 0.00 - no Open
329 1.7650189558589326 -1.04283 -32.4787 6 12 0 0.00 0.00 - no Open
379 1.969342891855111 -0.889133 -24.5333 2 11 0 0.00 0.00 - no Open
325 2.125064930305446 -1.21138 -36.9499 9 20 0 0.00 0.00 - no Open
370 2.6577378078182576 -0.783465 -23.9328 5 9 0 0.00 0.00 - no Open
401 2.8276500106851037 -0.751507 -24.4635 10 12 0 0.00 0.00 - no Open
339 3.4270672992810502 -0.865213 -25.4592 9 17 5 0.31 0.20 - no Open
388 3.555555808287048 -0.931199 -26.8835 15 17 0 0.00 0.00 - no Open
360 3.9357191430534906 -1.02887 -25.0561 14 17 0 0.00 0.00 - no Open
385 4.556515282102343 -0.781229 -24.3789 8 11 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 -30.273kcal/mol
Ligand efficiency (LE) -1.0812kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.207
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 28HA

Physicochemical properties
Molecular weight 429.9Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.57
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 23.06kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 22.68kcal/mol
Minimised FF energy -0.38kcal/mol

SASA & burial

✓ computed
SASA (unbound) 628.2Ų
Total solvent-accessible surface area of free ligand
BSA total 463.5Ų
Buried surface area upon binding
BSA apolar 241.2Ų
Hydrophobic contacts buried
BSA polar 222.3Ų
Polar contacts buried
Fraction buried 73.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 52.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2006.0Ų
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 851.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)