FAIRMol

Z56786752

Pose ID 3153 Compound 2085 Pose 443

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 Z56786752
PDB7PXX↗

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 medium Native strong SASA done
Strain ΔE
17.8 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.65, Jaccard 0.58, H-bond role recall 0.50
Burial
96%
Hydrophobic fit
75%
Reason: no major geometry red flags detected
3 protein-contact clashes 3 intramolecular clashes
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.460 kcal/mol/HA) ✓ Good fit quality (FQ -11.96) ✓ Strong H-bond network (9 bonds) ✓ Deep burial (96% SASA buried) ✓ Lipophilic contacts well-matched (75%) ✗ Moderate strain (17.8 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (5)
Score
-27.730
kcal/mol
LE
-1.460
kcal/mol/HA
Fit Quality
-11.96
FQ (Leeson)
HAC
19
heavy atoms
MW
269
Da
LogP
-1.00
cLogP
Strain ΔE
17.8 kcal/mol
SASA buried
96%
Lipo contact
75% BSA apolar/total
SASA unbound
450 Ų
Apolar buried
323 Ų

Interaction summary

HB 9 HY 12 PI 1 CLASH 3

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
Final rank1.726Score-27.730
Inter norm-1.522Intra norm0.062
Top1000noExcludedno
Contacts13H-bonds9
Artifact reasongeometry warning; 5 clashes; 1 protein clash; 1 severe cofactor-context clash
Residues
ARG17 ASP181 GLY225 LEU188 LEU226 LEU229 MET183 NDP302 PHE113 SER227 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 overlap11Native recall0.65
Jaccard0.58RMSD-
HB strict3Strict recall0.43
HB same residue+role3HB role recall0.50
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
456 -0.8575559526505838 -1.58974 -29.3357 6 15 0 0.00 0.00 - no Open
443 1.7262019837780336 -1.52158 -27.7304 9 13 11 0.65 0.50 - no Current
487 3.5785374152477725 -1.29144 -24.9451 11 15 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 -27.730kcal/mol
Ligand efficiency (LE) -1.4595kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -11.963
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 19HA

Physicochemical properties
Molecular weight 269.2Da
Lipinski: ≤ 500 Da
LogP (cLogP) -1.00
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 17.82kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 58.60kcal/mol
Minimised FF energy 40.79kcal/mol

SASA & burial

✓ computed
SASA (unbound) 450.4Ų
Total solvent-accessible surface area of free ligand
BSA total 430.2Ų
Buried surface area upon binding
BSA apolar 322.9Ų
Hydrophobic contacts buried
BSA polar 107.3Ų
Polar contacts buried
Fraction buried 95.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 75.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1497.0Ų
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 2179.4Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1019.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)