FAIRMol

Z275025498

Pose ID 5122 Compound 760 Pose 381

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
T08
T. brucei PTR1 T. brucei
Ligand Z275025498
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 high Native strong SASA done
Strain ΔE
11.4 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.58, Jaccard 0.48, H-bond role recall 0.20
Burial
90%
Hydrophobic fit
68%
Reason: no major geometry red flags detected
1 protein-contact clashes 35% of hydrophobic surface appears solvent-exposed (6/17 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.213 kcal/mol/HA) ✓ Good fit quality (FQ -11.45) ✓ Good H-bonds (4 bonds) ✓ Deep burial (90% SASA buried) ✓ Lipophilic contacts well-matched (68%) ✗ Moderate strain (11.4 kcal/mol) ✗ Geometry warnings ✗ Minor protein-contact clashes (4) ✗ Internal clashes (8)
Score
-33.957
kcal/mol
LE
-1.213
kcal/mol/HA
Fit Quality
-11.45
FQ (Leeson)
HAC
28
heavy atoms
MW
430
Da
LogP
3.57
cLogP
Strain ΔE
11.4 kcal/mol
SASA buried
90%
Lipo contact
68% BSA apolar/total
SASA unbound
664 Ų
Apolar buried
401 Ų

Interaction summary

HB 4 HY 16 PI 2 CLASH 1 ⚠ 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 (6/17 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 17 Buried (contacted) 11 Exposed 6 LogP 3.57 H-bonds 4
Exposed fragments: phenyl (6/6 atoms exposed)
Final rank0.468Score-33.957
Inter norm-1.153Intra norm-0.060
Top1000noExcludedno
Contacts15H-bonds4
Artifact reasongeometry warning; 8 clashes; 4 protein contact clashes
Residues
ARG14 ASP161 GLY205 LEU208 LEU209 LEU263 LYS13 MET163 NAP301 PHE97 PRO210 TRP221 TYR174 VAL206 VAL211

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 overlap11Native recall0.58
Jaccard0.48RMSD-
HB strict0Strict recall0.00
HB same residue+role1HB role recall0.20
HB same residue1HB residue recall0.20

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

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
381 0.4678678754036258 -1.1526 -33.9568 4 15 11 0.58 0.20 - no Current
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 0 0.00 0.00 - no Open
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 0 0.00 0.00 - 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 -33.957kcal/mol
Ligand efficiency (LE) -1.2127kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -11.449
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) 11.40kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 14.19kcal/mol
Minimised FF energy 2.80kcal/mol

SASA & burial

✓ computed
SASA (unbound) 663.6Ų
Total solvent-accessible surface area of free ligand
BSA total 594.1Ų
Buried surface area upon binding
BSA apolar 401.3Ų
Hydrophobic contacts buried
BSA polar 192.8Ų
Polar contacts buried
Fraction buried 89.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 67.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1556.2Ų
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 949.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)