FAIRMol

Z275025498

Pose ID 3039 Compound 760 Pose 329

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
T05
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
Weak SASA cached
Weak or marginal quality
Binding strong Geometry medium Native strong SASA done
Strain ΔE
32.5 kcal/mol
Protein clashes
2
Internal clashes
5
Native overlap
contact recall 0.59, Jaccard 0.53, H-bond role recall 0.33
Burial
88%
Hydrophobic fit
68%
Reason: no major geometry red flags detected
2 protein-contact clashes 5 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 ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.160 kcal/mol/HA) ✓ Good fit quality (FQ -10.95) ✓ Strong H-bond network (6 bonds) ✓ Deep burial (88% SASA buried) ✓ Lipophilic contacts well-matched (68%) ✗ Very high strain energy (32.5 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (10)
Score
-32.479
kcal/mol
LE
-1.160
kcal/mol/HA
Fit Quality
-10.95
FQ (Leeson)
HAC
28
heavy atoms
MW
430
Da
LogP
4.21
cLogP
Strain ΔE
32.5 kcal/mol
SASA buried
88%
Lipo contact
68% BSA apolar/total
SASA unbound
642 Ų
Apolar buried
381 Ų

Interaction summary

HB 6 HY 9 PI 2 CLASH 5 ⚠ 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 6
Exposed fragments: phenyl (6/6 atoms exposed)
Final rank1.765Score-32.479
Inter norm-1.043Intra norm-0.142
Top1000noExcludedno
Contacts12H-bonds6
Artifact reasongeometry warning; 10 clashes; 1 protein clash; 4 cofactor-context clashes; high strain Δ 32.5
Residues
ARG17 ARG39 GLY225 LEU188 LEU226 NDP302 PHE113 SER111 SER112 TYR194 VAL230 ARG287

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
NameligandContacts17
PoseOpen native poseHB0
IFP residues
ARG17 GLY225 HIS241 LEU188 LEU226 LEU229 LYS198 MET233 NDP302 PHE113 PRO115 SER111 SER227 TYR191 TYR194 VAL230 ARG287
Current overlap10Native recall0.59
Jaccard0.53RMSD-
HB strict2Strict recall0.29
HB same residue+role2HB role recall0.33
HB same residue3HB residue recall0.60

Protein summary

274 residues
Protein targetT05Atoms4108
Residues274Chains2
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 10 0.59 0.33 - no Current
379 1.969342891855111 -0.889133 -24.5333 2 11 10 0.59 0.17 - 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 -32.479kcal/mol
Ligand efficiency (LE) -1.1600kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.950
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) 32.50kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 54.77kcal/mol
Minimised FF energy 22.28kcal/mol

SASA & burial

✓ computed
SASA (unbound) 642.1Ų
Total solvent-accessible surface area of free ligand
BSA total 562.2Ų
Buried surface area upon binding
BSA apolar 381.1Ų
Hydrophobic contacts buried
BSA polar 181.1Ų
Polar contacts buried
Fraction buried 87.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 67.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1565.6Ų
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 1051.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)