FAIRMol

Z275025498

Pose ID 2412 Compound 760 Pose 379

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
T04
L. major PTR1 L. major
Ligand Z275025498
PDB7PXX↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
43.3 kcal/mol
Protein clashes
2
Internal clashes
3
Native overlap
contact recall 0.58, Jaccard 0.58, H-bond role recall 0.20
Burial
71%
Hydrophobic fit
59%
Reason: strain 43.3 kcal/mol
strain ΔE 43.3 kcal/mol 2 protein-contact clashes 3 intramolecular 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 ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.876 kcal/mol/HA) ✓ Good fit quality (FQ -8.27) ✓ Deep burial (71% SASA buried) ✗ Extreme strain energy (43.3 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (8)
Score
-24.533
kcal/mol
LE
-0.876
kcal/mol/HA
Fit Quality
-8.27
FQ (Leeson)
HAC
28
heavy atoms
MW
430
Da
LogP
4.21
cLogP
Strain ΔE
43.3 kcal/mol
SASA buried
71%
Lipo contact
59% BSA apolar/total
SASA unbound
642 Ų
Apolar buried
272 Ų

Interaction summary

HB 2 HY 11 PI 4 CLASH 3 ⚠ 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 4.21 H-bonds 2
Exposed fragments: phenyl (6/6 atoms exposed)
Final rank1.969Score-24.533
Inter norm-0.889Intra norm0.013
Top1000noExcludedno
Contacts11H-bonds2
Artifact reasongeometry warning; 8 clashes; 1 protein clash; 1 cofactor-context clash; high strain Δ 43.3
Residues
ARG17 ASP181 GLY225 HIS241 LEU188 LEU226 LEU229 NDP302 PHE113 TYR191 TYR194

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name7PXXContacts19
PoseOpen native poseHB0
IFP residues
ARG17 ASP181 GLY225 HIS241 LEU188 LEU226 LEU229 LYS198 MET233 NDP302 PHE113 PRO115 SER111 SER112 SER227 TYR191 TYR194 VAL230 ARG287
Current overlap11Native recall0.58
Jaccard0.58RMSD-
HB strict1Strict recall0.17
HB same residue+role1HB role recall0.20
HB same residue1HB residue recall0.20

Protein summary

308 residues
Protein targetT04Atoms4210
Residues308Chains3
Residue summaryLEU:494; ALA:421; ARG:384; VAL:368; THR:295; TYR:231; SER:198; PRO:196; ILE:190; LYS:176; ASN:154; GLU:150; GLY:126; PHE:120; HIS:119; ASP:108

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:NDP302

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 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 11 0.58 0.40 - no Open
379 1.969342891855111 -0.889133 -24.5333 2 11 11 0.58 0.20 - no Current
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 -24.533kcal/mol
Ligand efficiency (LE) -0.8762kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.272
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 28HA

Physicochemical properties
Molecular weight 429.9Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.21
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 43.33kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 65.15kcal/mol
Minimised FF energy 21.82kcal/mol

SASA & burial

✓ computed
SASA (unbound) 642.2Ų
Total solvent-accessible surface area of free ligand
BSA total 458.1Ų
Buried surface area upon binding
BSA apolar 271.8Ų
Hydrophobic contacts buried
BSA polar 186.3Ų
Polar contacts buried
Fraction buried 71.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 59.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1511.1Ų
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 2179.4Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1102.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)