Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
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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
36.7 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.67, Jaccard 0.56, H-bond role recall 0.40
Reason: no major geometry red flags detected
1 protein-contact clashes
73% of hydrophobic surface is solvent-exposed (16/22 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.606 kcal/mol/HA)
✓ Good fit quality (FQ -6.06)
✓ Strong H-bond network (8 bonds)
✓ Deep burial (76% SASA buried)
✓ Lipophilic contacts well-matched (78%)
✗ Very high strain energy (36.7 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (13)
Score
-20.605
kcal/mol
LE
-0.606
kcal/mol/HA
Fit Quality
-6.06
FQ (Leeson)
HAC
34
heavy atoms
MW
486
Da
LogP
-0.47
cLogP
Interaction summary
HB 8
HY 2
PI 0
CLASH 1
⚠ Exposure 72%
Interaction summary
HB 8
HY 2
PI 0
CLASH 1
⚠ Exposure 72%
HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
PI · π–π interactions
No pi · π–π interactions detected for this pose.
HY · Hydrophobic contacts
CLASH · Clashes
Solvent-exposed hydrophobic surface — desolvation penalty likely
73% of hydrophobic surface is solvent-exposed (16/22 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Non-polar atoms 22
Buried (contacted) 6
Exposed 16
LogP -0.47
H-bonds 8
Exposed fragments:
pyridyl (5/6 atoms exposed)pyridyl (4/6 atoms exposed)pyridyl (5/6 atoms exposed)aliphatic chain/group (4 atoms exposed)
| Final rank | 4.294 | Score | -20.605 |
|---|---|---|---|
| Inter norm | -0.784 | Intra norm | 0.178 |
| Top1000 | no | Excluded | no |
| Contacts | 13 | H-bonds | 8 |
| Artifact reason | geometry warning; 13 clashes; 2 protein clashes; high strain Δ 36.6 | ||
| Residues |
ARG22
ARG242
ARG337
ASP243
ASP385
GLU384
LEU25
LEU382
PHE284
SER282
THR21
THR241
THR285
| ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 1NJJ | Contacts | 15 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ARG22
ARG242
ARG337
ARG342
ASP243
ASP385
GLN341
GLU384
LEU25
LEU339
LEU382
PRO340
PRO344
SER282
THR241
| ||
| Current overlap | 10 | Native recall | 0.67 |
| Jaccard | 0.56 | RMSD | - |
| HB strict | 1 | Strict recall | 0.17 |
| HB same residue+role | 2 | HB role recall | 0.40 |
| HB same residue | 2 | HB residue recall | 0.40 |
Protein summary
398 residues
| Protein target | T14 | Atoms | 6140 |
|---|---|---|---|
| Residues | 398 | Chains | 1 |
| Residue summary | VAL:592; LEU:513; LYS:484; ARG:432; PHE:420; ILE:418; ASP:349; THR:322; TYR:315; PRO:308; GLU:301; ALA:290; SER:253; GLY:217; ASN:210; GLN:170 | ||
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:ORX602
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 118 | 1.6221210217379594 | -0.802718 | -20.4321 | 3 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 128 | 1.7505082341560974 | -0.864138 | -28.5222 | 5 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 87 | 4.153044674428568 | -0.762765 | -23.1 | 9 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 138 | 4.293758451486025 | -0.784325 | -20.6052 | 8 | 13 | 10 | 0.67 | 0.40 | - | no | Current |
| 76 | 4.593964288158693 | -1.01947 | -32.3861 | 11 | 27 | 0 | 0.00 | 0.00 | - | no | Open |
| 130 | 5.298055146730686 | -0.689012 | -17.2193 | 9 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-20.605kcal/mol
Ligand efficiency (LE)
-0.6060kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.064
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
34HA
Physicochemical properties
Molecular weight
486.0Da
Lipinski: ≤ 500 Da
LogP (cLogP)
-0.47
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
36.67kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
168.78kcal/mol
Minimised FF energy
132.11kcal/mol
SASA & burial
✓ computed
SASA (unbound)
757.6Ų
Total solvent-accessible surface area of free ligand
BSA total
578.5Ų
Buried surface area upon binding
BSA apolar
450.5Ų
Hydrophobic contacts buried
BSA polar
128.1Ų
Polar contacts buried
Fraction buried
76.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
77.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2554.2Ų
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
3349.0Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1406.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)